rs2814944

Variant names:

• chr6-34585020-G-A
• rs2814944

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 0.196 in 151,936 control chromosomes in the GnomAD database, including 3,448 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 0.20 (3448 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 72 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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: 0.196 AC: 29749 AN: 151818 Hom.: 3442 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.196 AC: 29780 AN: 151936 Hom.: 3448 Cov.: 32 AF XY: 0.196 AC XY: 14526 AN XY: 74274

African (AFR) AF: 0.314 AC: 13019 AN: 41454

American (AMR) AF: 0.137 AC: 2094 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3464

East Asian (EAS) AF: 0.0118 AC: 61 AN: 5184

South Asian (SAS) AF: 0.0962 AC: 464 AN: 4822

European-Finnish (FIN) AF: 0.222 AC: 2340 AN: 10546

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10594 AN: 67880

Other (OTH) AF: 0.188 AC: 396 AN: 2110

Alfa AF: 0.162 Hom.: 7805

Bravo AF: 0.195

Asia WGS AF: 0.0630 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.41
DANN	Benign	0.77
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2814944; hg19: chr6-34552797;