rs607613

Variant names:

• chr5-31388010-T-C
• rs607613

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 0.858 in 152,100 control chromosomes in the GnomAD database, including 56,244 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 0.86 (56244 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 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: 0.858 AC: 130361 AN: 151982 Hom.: 56193 Cov.: 31

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.858 AC: 130470 AN: 152100 Hom.: 56244 Cov.: 31 AF XY: 0.859 AC XY: 63837 AN XY: 74358

African (AFR) AF: 0.928 AC: 38506 AN: 41476

American (AMR) AF: 0.863 AC: 13190 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2505 AN: 3472

East Asian (EAS) AF: 0.773 AC: 3980 AN: 5150

South Asian (SAS) AF: 0.837 AC: 4024 AN: 4810

European-Finnish (FIN) AF: 0.877 AC: 9293 AN: 10600

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56108 AN: 67984

Other (OTH) AF: 0.848 AC: 1793 AN: 2114

Alfa AF: 0.834 Hom.: 65193

Bravo AF: 0.859

Asia WGS AF: 0.799 AC: 2780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.75
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs607613; hg19: chr5-31388117;