1-91677677-A-G

Variant names:

• chr1-91677677-A-G
• rs2810894

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 0.715 in 151,942 control chromosomes in the GnomAD database, including 39,594 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 0.71 (39594 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 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: 0.715 AC: 108490 AN: 151826 Hom.: 39541 Cov.: 30

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.715 AC: 108597 AN: 151942 Hom.: 39594 Cov.: 30 AF XY: 0.714 AC XY: 52999 AN XY: 74272

African (AFR) AF: 0.855 AC: 35450 AN: 41442

American (AMR) AF: 0.675 AC: 10314 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2363 AN: 3470

East Asian (EAS) AF: 0.513 AC: 2655 AN: 5176

South Asian (SAS) AF: 0.740 AC: 3560 AN: 4808

European-Finnish (FIN) AF: 0.627 AC: 6592 AN: 10508

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45332 AN: 67956

Other (OTH) AF: 0.703 AC: 1482 AN: 2108

Alfa AF: 0.677 Hom.: 40952

Bravo AF: 0.719

Asia WGS AF: 0.636 AC: 2214 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.70
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs2810894; hg19: chr1-92143234;