rs2817957

Variant names:

• chr6-120864232-T-C
• rs2817957

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 0.44 in 151,410 control chromosomes in the GnomAD database, including 17,384 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 0.44 (17384 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.440 AC: 66573 AN: 151290 Hom.: 17335 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.440 AC: 66687 AN: 151410 Hom.: 17384 Cov.: 32 AF XY: 0.441 AC XY: 32673 AN XY: 74038

African (AFR) AF: 0.684 AC: 28336 AN: 41402

American (AMR) AF: 0.562 AC: 8534 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1323 AN: 3458

East Asian (EAS) AF: 0.605 AC: 3121 AN: 5156

South Asian (SAS) AF: 0.528 AC: 2538 AN: 4810

European-Finnish (FIN) AF: 0.203 AC: 2142 AN: 10556

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19483 AN: 67532

Other (OTH) AF: 0.436 AC: 915 AN: 2100

Alfa AF: 0.377 Hom.: 1561

Bravo AF: 0.477

Asia WGS AF: 0.586 AC: 2038 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2817957; hg19: chr6-121185378;