rs643009

chr1-229774990-G-Achr1-229774990-G-Cchr1-229774990-G-T

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 0.57 in 150,232 control chromosomes in the GnomAD database, including 25,193 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 0.57 (25193 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.570 AC: 85639 AN: 150122 Hom.: 25173 Cov.: 27

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.603

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.570 AC: 85703 AN: 150232 Hom.: 25193 Cov.: 27 AF XY: 0.575 AC XY: 42114 AN XY: 73180

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.581

Alfa AF: 0.590 Hom.: 54500

Bravo AF: 0.575

Asia WGS AF: 0.676 AC: 2331 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.2
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs643009; hg19: chr1-229910737;