rs2372008

Variant names:

• chr2-35576048-G-A
• rs2372008
• ENST00000741472.1:n.81+1583C>T

Variant summary

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

The ENST00000741472.1(ENSG00000296736):​n.81+1583C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,892 control chromosomes in the GnomAD database, including 22,859 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 0.54 (22859 hom., cov: 30)
• Consequence: ENSG00000296736 ENST00000741472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 3 publications found

Genes affected

ENSG00000296736 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741472.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296736	ENST00000741472.1		n.81+1583C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81500 AN: 151776 Hom.: 22842 Cov.: 30

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.537 AC: 81543 AN: 151892 Hom.: 22859 Cov.: 30 AF XY: 0.541 AC XY: 40134 AN XY: 74216

African (AFR) AF: 0.356 AC: 14763 AN: 41416

American (AMR) AF: 0.592 AC: 9043 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1962 AN: 3466

East Asian (EAS) AF: 0.676 AC: 3459 AN: 5116

South Asian (SAS) AF: 0.599 AC: 2887 AN: 4818

European-Finnish (FIN) AF: 0.630 AC: 6631 AN: 10522

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40848 AN: 67966

Other (OTH) AF: 0.558 AC: 1179 AN: 2114

Alfa AF: 0.570 Hom.: 4420

Bravo AF: 0.526

Asia WGS AF: 0.601 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.53
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2372008; hg19: chr2-35801114;