1-21494497-A-G

Variant names:

• chr1-21494497-A-G
• rs10799701

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.519

Alfa AF: 0.546 Hom.: 25414

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10799701; hg19: chr1-21820990;