rs2279768

Variant names:

• chr10-2937459-G-C
• rs2279768

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 0.167 in 152,158 control chromosomes in the GnomAD database, including 2,277 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 0.17 (2277 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.209 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: 0.167 AC: 25346 AN: 152040 Hom.: 2277 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.0884

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.167 AC: 25347 AN: 152158 Hom.: 2277 Cov.: 33 AF XY: 0.167 AC XY: 12400 AN XY: 74382

African (AFR) AF: 0.115 AC: 4781 AN: 41514

American (AMR) AF: 0.127 AC: 1938 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 827 AN: 3468

East Asian (EAS) AF: 0.0886 AC: 459 AN: 5180

South Asian (SAS) AF: 0.220 AC: 1058 AN: 4818

European-Finnish (FIN) AF: 0.210 AC: 2224 AN: 10578

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13502 AN: 67998

Other (OTH) AF: 0.180 AC: 379 AN: 2110

Alfa AF: 0.192 Hom.: 376

Bravo AF: 0.153

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.62
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2279768; hg19: chr10-2979651;