rs601509

chr6-153957473-C-T

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 0.727 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.683

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs601509; hg19: chr6-154278608;