rs912765

Variant names:

• chr1-87178264-C-T
• rs912765

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 0.448 in 152,038 control chromosomes in the GnomAD database, including 15,426 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 0.45 (15426 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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: 0.448 AC: 68036 AN: 151920 Hom.: 15411 Cov.: 33

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.448 AC: 68090 AN: 152038 Hom.: 15426 Cov.: 33 AF XY: 0.441 AC XY: 32755 AN XY: 74312

African (AFR) AF: 0.493 AC: 20432 AN: 41478

American (AMR) AF: 0.446 AC: 6814 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1672 AN: 5164

South Asian (SAS) AF: 0.247 AC: 1187 AN: 4810

European-Finnish (FIN) AF: 0.451 AC: 4769 AN: 10566

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30543 AN: 67974

Other (OTH) AF: 0.441 AC: 925 AN: 2098

Alfa AF: 0.442 Hom.: 15788

Bravo AF: 0.455

Asia WGS AF: 0.309 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.0
DANN	Benign	0.71
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs912765; hg19: chr1-87643947;