1-23531510-T-G

Position:

• chr1-23531510-T-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 0.713 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;