4-124731512-G-C

Variant names:

• chr4-124731512-G-C
• rs17008522

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.674 in 151,658 control chromosomes in the GnomAD database, including 34,756 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 0.67 (34756 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.731 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102123 AN: 151538 Hom.: 34722 Cov.: 29

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.674 AC: 102216 AN: 151658 Hom.: 34756 Cov.: 29 AF XY: 0.667 AC XY: 49392 AN XY: 74094

African (AFR) AF: 0.738 AC: 30486 AN: 41328

American (AMR) AF: 0.684 AC: 10420 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2274 AN: 3466

East Asian (EAS) AF: 0.495 AC: 2534 AN: 5120

South Asian (SAS) AF: 0.686 AC: 3290 AN: 4794

European-Finnish (FIN) AF: 0.513 AC: 5391 AN: 10500

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45717 AN: 67902

Other (OTH) AF: 0.661 AC: 1389 AN: 2102

Alfa AF: 0.545 Hom.: 1417

Bravo AF: 0.686

Asia WGS AF: 0.605 AC: 2104 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.28
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs17008522; hg19: chr4-125652667;