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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.0327

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0774

Gnomad4 FIN AF: 0.0121

Gnomad4 NFE AF: 0.0233

Gnomad4 OTH AF: 0.0451

Alfa AF: 0.0296 Hom.: 176

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2774292; hg19: chr1-114715584;