1-23531510-T-G

Variant names:

• chr1-23531510-T-G
• rs2742976

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 0.713 in 151,570 control chromosomes in the GnomAD database, including 39,503 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 0.71 (39503 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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: 0.713 AC: 107989 AN: 151452 Hom.: 39463 Cov.: 28

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.713 AC: 108082 AN: 151570 Hom.: 39503 Cov.: 28 AF XY: 0.714 AC XY: 52831 AN XY: 74038

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.719

Alfa AF: 0.637 Hom.: 3955

Bravo AF: 0.726

Asia WGS AF: 0.809 AC: 2814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.93
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2742976; hg19: chr1-23858002;