rs2817952

Variant names:

• chr6-120865954-C-G
• rs2817952

Your query was ambiguous. Multiple possible variants found:

• chr6-120865954-C-G
• chr6-120865954-C-T

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 151,382 control chromosomes in the GnomAD database, including 17,372 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 (17372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• 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: 66510 AN: 151264 Hom.: 17324 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.288

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: 66622 AN: 151382 Hom.: 17372 Cov.: 32 AF XY: 0.441 AC XY: 32625 AN XY: 73996

African (AFR) AF: 0.684 AC: 28323 AN: 41386

American (AMR) AF: 0.561 AC: 8532 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1321 AN: 3456

East Asian (EAS) AF: 0.603 AC: 3113 AN: 5160

South Asian (SAS) AF: 0.528 AC: 2539 AN: 4810

European-Finnish (FIN) AF: 0.201 AC: 2125 AN: 10546

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

European-Non Finnish (NFE) AF: 0.288 AC: 19457 AN: 67516

Other (OTH) AF: 0.435 AC: 917 AN: 2106

Alfa AF: 0.377 Hom.: 1560

Bravo AF: 0.477

Asia WGS AF: 0.587 AC: 2039 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	10
DANN	Benign	0.75
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs2817952; hg19: chr6-121187100;