rs2760994

Variant names:

• chr6-32606531-C-T
• rs2760994

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 0.627 in 151,898 control chromosomes in the GnomAD database, including 30,143 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 0.63 (30143 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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: 0.627 AC: 95209 AN: 151780 Hom.: 30105 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.627 AC: 95298 AN: 151898 Hom.: 30143 Cov.: 31 AF XY: 0.629 AC XY: 46648 AN XY: 74214

African (AFR) AF: 0.647 AC: 26781 AN: 41386

American (AMR) AF: 0.686 AC: 10489 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2299 AN: 3470

East Asian (EAS) AF: 0.761 AC: 3929 AN: 5160

South Asian (SAS) AF: 0.560 AC: 2693 AN: 4812

European-Finnish (FIN) AF: 0.607 AC: 6399 AN: 10544

Middle Eastern (MID) AF: 0.753 AC: 220 AN: 292

European-Non Finnish (NFE) AF: 0.599 AC: 40723 AN: 67940

Other (OTH) AF: 0.641 AC: 1348 AN: 2102

Alfa AF: 0.623 Hom.: 15419

Bravo AF: 0.635

Asia WGS AF: 0.633 AC: 2204 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	0.40
DANN	Benign	0.77
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2760994; hg19: chr6-32574308;