Variant 7-106625119-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000490856.5(ENSG00000243797):n.109-14656G>C 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 0.708 in 151,946 control chromosomes in the GnomAD database, including 38,270 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.71 ( 38270 hom., cov: 31)

Consequence

ENST00000490856.5 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.541

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375440	XR_007060468.1 linkuse as main transcript	n.200-594C>G		intron_variant, non_coding_transcript_variant
LOC105375440	XR_927844.3 linkuse as main transcript	n.200-594C>G		intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect	TSL
ENST00000490856.5 linkuse as main transcript	n.109-14656G>C	intron_variant, non_coding_transcript_variant	4
ENST00000652725.1 linkuse as main transcript	n.187-594C>G	intron_variant, non_coding_transcript_variant
ENST00000485282.5 linkuse as main transcript	n.150-9348G>C	intron_variant, non_coding_transcript_variant	3
ENST00000592441.1 linkuse as main transcript	n.173-14656G>C	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.707

AC:

107405

AN:

151828

Hom.:

38221

Cov.:

show subpopulations

Gnomad AFR

AF:

0.754

Gnomad AMI

AF:

0.746

Gnomad AMR

AF:

0.699

Gnomad ASJ

AF:

0.644

Gnomad EAS

AF:

0.468

Gnomad SAS

AF:

0.589

Gnomad FIN

AF:

0.703

Gnomad MID

AF:

0.696

Gnomad NFE

AF:

0.711

Gnomad OTH

AF:

0.701

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.708

AC:

107516

AN:

151946

Hom.:

38270

Cov.:

AF XY:

0.706

AC XY:

52370

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.754

Gnomad4 AMR

AF:

0.700

Gnomad4 ASJ

AF:

0.644

Gnomad4 EAS

AF:

0.469

Gnomad4 SAS

AF:

0.587

Gnomad4 FIN

AF:

0.703

Gnomad4 NFE

AF:

0.711

Gnomad4 OTH

AF:

0.703

Alfa

AF:

0.646

Hom.:

2122

Bravo

AF:

0.707

Asia WGS

AF:

0.548

AC:

1906

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.6

DANN

Benign

0.64

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over