1-7947656-A-G

Variant names:

• chr1-7947656-A-G
• rs2493215

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 0.373 in 152,162 control chromosomes in the GnomAD database, including 11,837 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 0.37 (11837 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 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: 0.373 AC: 56773 AN: 152044 Hom.: 11837 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.373 AC: 56780 AN: 152162 Hom.: 11837 Cov.: 33 AF XY: 0.376 AC XY: 27960 AN XY: 74376

African (AFR) AF: 0.181 AC: 7522 AN: 41534

American (AMR) AF: 0.380 AC: 5806 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1586 AN: 3468

East Asian (EAS) AF: 0.383 AC: 1981 AN: 5178

South Asian (SAS) AF: 0.625 AC: 3016 AN: 4826

European-Finnish (FIN) AF: 0.412 AC: 4352 AN: 10574

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30898 AN: 67986

Other (OTH) AF: 0.421 AC: 887 AN: 2108

Alfa AF: 0.434 Hom.: 8198

Bravo AF: 0.355

Asia WGS AF: 0.472 AC: 1643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.60
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2493215; hg19: chr1-8007716; COSMIC: COSV74213286;