rs607613

Positions:

• chr5-31388010-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;