Variant 1-150551891-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_019032.6(ADAMTSL4):c.-84-299dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0526 in 118,386 control chromosomes in the GnomAD database, including 275 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.055 ( 275 hom., cov: 30)

Exomes 𝑓: 0.046 ( 0 hom. )

Consequence

ADAMTSL4
NM_019032.6 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.855

Variant links:

Genes affected

ADAMTSL4 (HGNC:19706): (ADAMTS like 4) This gene is a member of ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs)-like gene family and encodes a protein with seven thrombospondin type 1 repeats. The thrombospondin type 1 repeat domain is found in many proteins with diverse biological functions including cellular adhesion, angiogenesis, and patterning of the developing nervous system. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Sep 2014]

ADAMTSL4 links:

ADAMTSL4-AS2 (HGNC:40895): (ADAMTSL4 antisense RNA 2)

ADAMTSL4-AS2 links:

MIR4257 (HGNC:38312): (microRNA 4257) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR4257 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-150551891-C-CA is Benign according to our data. Variant chr1-150551891-C-CA is described in ClinVar as [Benign]. Clinvar id is 1263408.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
ADAMTSL4	NM_019032.6 linkuse as main transcript	c.-84-299dup	intron_variant	ENST00000271643.9	NP_061905.2
ADAMTSL4-AS2	XR_001738229.2 linkuse as main transcript	n.211-3142_211-3141insT	intron_variant, non_coding_transcript_variant
MIR4257	NR_036211.1 linkuse as main transcript		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
ADAMTSL4	ENST00000271643.9 linkuse as main transcript	c.-84-299dup	intron_variant	5	NM_019032.6	ENSP00000271643	P1	Q6UY14-1
ADAMTSL4-AS2	ENST00000442435.3 linkuse as main transcript	n.476+2643_476+2644insT	intron_variant, non_coding_transcript_variant	5
MIR4257	ENST00000581735.1 linkuse as main transcript		upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0544

AC:

5032

AN:

92466

Hom.:

275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.167

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0280

Gnomad ASJ

AF:

0.0409

Gnomad EAS

AF:

0.00940

Gnomad SAS

AF:

0.00460

Gnomad FIN

AF:

0.00569

Gnomad MID

AF:

0.0278

Gnomad NFE

AF:

0.00383

Gnomad OTH

AF:

0.0405

GnomAD3 exomes

AF:

0.0763

AC:

289

AN:

3788

Hom.:

AF XY:

0.0653

AC XY:

132

AN XY:

2022

show subpopulations

Gnomad AFR exome

AF:

0.140

Gnomad AMR exome

AF:

0.0667

Gnomad ASJ exome

AF:

0.102

Gnomad EAS exome

AF:

0.0833

Gnomad SAS exome

AF:

0.0354

Gnomad NFE exome

AF:

0.0769

Gnomad OTH exome

AF:

0.0610

GnomAD4 exome

AF:

0.0459

AC:

1189

AN:

25900

Hom.:

Cov.:

AF XY:

0.0453

AC XY:

603

AN XY:

13318

show subpopulations

Gnomad4 AFR exome

AF:

0.0995

Gnomad4 AMR exome

AF:

0.0432

Gnomad4 ASJ exome

AF:

0.0534

Gnomad4 EAS exome

AF:

0.0460

Gnomad4 SAS exome

AF:

0.0512

Gnomad4 FIN exome

AF:

0.0451

Gnomad4 NFE exome

AF:

0.0426

Gnomad4 OTH exome

AF:

0.0533

GnomAD4 genome

AF:

0.0545

AC:

5042

AN:

92486

Hom.:

275

Cov.:

AF XY:

0.0541

AC XY:

2359

AN XY:

43616

show subpopulations

Gnomad4 AFR

AF:

0.168

Gnomad4 AMR

AF:

0.0280

Gnomad4 ASJ

AF:

0.0409

Gnomad4 EAS

AF:

0.00942

Gnomad4 SAS

AF:

0.00463

Gnomad4 FIN

AF:

0.00569

Gnomad4 NFE

AF:

0.00383

Gnomad4 OTH

AF:

0.0401

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 03, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over