Variant rs62093482 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The XR_007066326.1(LOC124904277):n.129-3241G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0221 in 508,938 control chromosomes in the GnomAD database, including 158 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.018 ( 34 hom., cov: 33)

Exomes 𝑓: 0.024 ( 124 hom. )

Consequence

LOC124904277
XR_007066326.1 intron, non_coding_transcript

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.482

Variant links:

Genes affected

LOC124904277 (HGNC:):

LOC124904277 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 18-31598936-C-T is Benign according to our data. Variant chr18-31598936-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 892146.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0183 (2785/152192) while in subpopulation NFE AF= 0.0285 (1939/68014). AF 95% confidence interval is 0.0275. There are 34 homozygotes in gnomad4. There are 1320 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 34 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904277	XR_007066326.1 linkuse as main transcript	n.129-3241G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.0183

AC:

2788

AN:

152074

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00527

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0151

Gnomad ASJ

AF:

0.0130

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.0180

Gnomad FIN

AF:

0.0197

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0285

Gnomad OTH

AF:

0.0249

GnomAD4 exome

AF:

0.0237

AC:

8455

AN:

356746

Hom.:

124

Cov.:

AF XY:

0.0232

AC XY:

4400

AN XY:

189844

show subpopulations

Gnomad4 AFR exome

AF:

0.00590

Gnomad4 AMR exome

AF:

0.0116

Gnomad4 ASJ exome

AF:

0.0149

Gnomad4 EAS exome

AF:

0.000543

Gnomad4 SAS exome

AF:

0.0212

Gnomad4 FIN exome

AF:

0.0221

Gnomad4 NFE exome

AF:

0.0293

Gnomad4 OTH exome

AF:

0.0217

GnomAD4 genome

AF:

0.0183

AC:

2785

AN:

152192

Hom.:

Cov.:

AF XY:

0.0177

AC XY:

1320

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.00525

Gnomad4 AMR

AF:

0.0150

Gnomad4 ASJ

AF:

0.0130

Gnomad4 EAS

AF:

0.000966

Gnomad4 SAS

AF:

0.0178

Gnomad4 FIN

AF:

0.0197

Gnomad4 NFE

AF:

0.0285

Gnomad4 OTH

AF:

0.0242

Alfa

AF:

0.0255

Hom.:

Bravo

AF:

0.0169

Asia WGS

AF:

0.00722

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Familial amyloid neuropathy

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.7

DANN

Benign

0.75

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