rs596359

Variant names:

• chr6-153135918-C-T
• rs596359

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 0.544 in 151,944 control chromosomes in the GnomAD database, including 23,107 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 0.54 (23107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 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: 0.543 AC: 82492 AN: 151826 Hom.: 23069 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.544 AC: 82586 AN: 151944 Hom.: 23107 Cov.: 32 AF XY: 0.539 AC XY: 40008 AN XY: 74262

African (AFR) AF: 0.664 AC: 27503 AN: 41408

American (AMR) AF: 0.524 AC: 7997 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1801 AN: 3466

East Asian (EAS) AF: 0.243 AC: 1253 AN: 5158

South Asian (SAS) AF: 0.333 AC: 1600 AN: 4812

European-Finnish (FIN) AF: 0.549 AC: 5793 AN: 10546

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34906 AN: 67978

Other (OTH) AF: 0.556 AC: 1173 AN: 2110

Alfa AF: 0.518 Hom.: 10518

Bravo AF: 0.548

Asia WGS AF: 0.352 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.59
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs596359; hg19: chr6-153457053; COSMIC: COSV52811114;