1-23531510-T-G

Variant names:

• chr1-23531510-T-G
• rs2742976
• ENST00000826972.1:n.203+4440T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000826972.1(ENSG00000307540):​n.203+4440T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000307540 ENST00000826972.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 10 publications found

Genes affected

ENSG00000307540 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000307540	ENST00000826972.1	n.203+4440T>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.857 AC: 35478 AN: 41382

American (AMR) AF: 0.677 AC: 10316 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2791 AN: 3466

East Asian (EAS) AF: 0.930 AC: 4767 AN: 5124

South Asian (SAS) AF: 0.788 AC: 3761 AN: 4770

European-Finnish (FIN) AF: 0.588 AC: 6152 AN: 10464

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42402 AN: 67810

Other (OTH) AF: 0.719 AC: 1515 AN: 2106

Alfa AF: 0.645 Hom.: 4221

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
PhyloP100		-2.1
PromoterAI		-0.20	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2742976; hg19: chr1-23858002;