rs2774292

Variant names:

• chr1-114172962-G-A
• rs2774292

Your query was ambiguous. Multiple possible variants found:

• chr1-114172962-G-A
• chr1-114172962-G-C

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 0.0584 in 151,970 control chromosomes in the GnomAD database, including 504 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 0.058 (504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 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: 0.0582 AC: 8838 AN: 151852 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0327

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0233

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0584 AC: 8871 AN: 151970 Hom.: 504 Cov.: 32 AF XY: 0.0571 AC XY: 4242 AN XY: 74298

African (AFR) AF: 0.143 AC: 5926 AN: 41360

American (AMR) AF: 0.0327 AC: 499 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.0774 AC: 373 AN: 4820

European-Finnish (FIN) AF: 0.0121 AC: 128 AN: 10574

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0233 AC: 1583 AN: 67996

Other (OTH) AF: 0.0451 AC: 95 AN: 2108

Alfa AF: 0.0349 Hom.: 722

Bravo AF: 0.0618

Asia WGS AF: 0.0400 AC: 139 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.65
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2774292; hg19: chr1-114715584;