rs1612904

Positions:

• chr6-32701241-C-A
• chr6-32701241-C-G

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 0.67 in 151,928 control chromosomes in the GnomAD database, including 34,579 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 0.67 (34579 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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: 0.670 AC: 101711 AN: 151810 Hom.: 34553 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.670 AC: 101787 AN: 151928 Hom.: 34579 Cov.: 31 AF XY: 0.674 AC XY: 50055 AN XY: 74248

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.716

Alfa AF: 0.647 Hom.: 24101

Bravo AF: 0.679

Asia WGS AF: 0.834 AC: 2902 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.48
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1612904; hg19: chr6-32669018;