rs601509

Variant names:

• chr6-153957473-C-T
• rs601509

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 0.727 in 151,998 control chromosomes in the GnomAD database, including 40,352 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 0.73 (40352 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.756 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: 0.727 AC: 110431 AN: 151880 Hom.: 40346 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.727 AC: 110484 AN: 151998 Hom.: 40352 Cov.: 31 AF XY: 0.731 AC XY: 54291 AN XY: 74292

African (AFR) AF: 0.763 AC: 31615 AN: 41436

American (AMR) AF: 0.679 AC: 10373 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2185 AN: 3472

East Asian (EAS) AF: 0.755 AC: 3880 AN: 5138

South Asian (SAS) AF: 0.764 AC: 3679 AN: 4818

European-Finnish (FIN) AF: 0.792 AC: 8382 AN: 10582

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.707 AC: 48021 AN: 67958

Other (OTH) AF: 0.683 AC: 1443 AN: 2112

Alfa AF: 0.708 Hom.: 4743

Bravo AF: 0.719

Asia WGS AF: 0.729 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.7
DANN	Benign	0.88
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs601509; hg19: chr6-154278608;