rs607613

Variant names:

• chr5-31388010-T-C
• rs607613

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.848

Alfa AF: 0.828 Hom.: 48850

Bravo AF: 0.859

Asia WGS AF: 0.799 AC: 2780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs607613; hg19: chr5-31388117;