1-202931424-C-T

Variant names:

• chr1-202931424-C-T
• rs6672643

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 0.836 in 152,028 control chromosomes in the GnomAD database, including 53,456 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 0.84 (53456 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 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: 0.836 AC: 126927 AN: 151910 Hom.: 53399 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.836 AC: 127040 AN: 152028 Hom.: 53456 Cov.: 31 AF XY: 0.840 AC XY: 62465 AN XY: 74336

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.950

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.839

Alfa AF: 0.858 Hom.: 6998

Bravo AF: 0.826

Asia WGS AF: 0.858 AC: 2983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6672643; hg19: chr1-202900552; COSMIC: COSV66125256;