rs2791476

Variant names:

• chr1-86545769-G-A
• rs2791476

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 0.477 in 152,030 control chromosomes in the GnomAD database, including 21,407 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 0.48 (21407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 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: 0.476 AC: 72345 AN: 151914 Hom.: 21354 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.477 AC: 72448 AN: 152030 Hom.: 21407 Cov.: 32 AF XY: 0.477 AC XY: 35435 AN XY: 74278

African (AFR) AF: 0.824 AC: 34197 AN: 41516

American (AMR) AF: 0.320 AC: 4883 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1333 AN: 3464

East Asian (EAS) AF: 0.749 AC: 3876 AN: 5178

South Asian (SAS) AF: 0.515 AC: 2481 AN: 4814

European-Finnish (FIN) AF: 0.292 AC: 3073 AN: 10528

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21193 AN: 67946

Other (OTH) AF: 0.453 AC: 954 AN: 2104

Alfa AF: 0.397 Hom.: 1840

Bravo AF: 0.491

Asia WGS AF: 0.634 AC: 2205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.37
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2791476; hg19: chr1-87011452;