chr1-21494497-A-G

Variant names:

• chr1-21494497-A-G
• rs10799701

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 0.473 in 152,024 control chromosomes in the GnomAD database, including 18,685 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 0.47 (18685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 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: 0.474 AC: 71982 AN: 151906 Hom.: 18687 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.473 AC: 71981 AN: 152024 Hom.: 18685 Cov.: 31 AF XY: 0.477 AC XY: 35461 AN XY: 74292

African (AFR) AF: 0.248 AC: 10267 AN: 41468

American (AMR) AF: 0.568 AC: 8673 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1975 AN: 3470

East Asian (EAS) AF: 0.677 AC: 3498 AN: 5164

South Asian (SAS) AF: 0.513 AC: 2470 AN: 4816

European-Finnish (FIN) AF: 0.529 AC: 5589 AN: 10566

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37826 AN: 67958

Other (OTH) AF: 0.519 AC: 1093 AN: 2106

Alfa AF: 0.533 Hom.: 69204

Bravo AF: 0.466

Asia WGS AF: 0.529 AC: 1840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.73
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs10799701; hg19: chr1-21820990;