1-21494497-A-G

Position:

• chr1-21494497-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;