rs2681019

Variant names:

• chr2-22964632-C-A
• rs2681019
• ENST00000723051.1:n.97+37103G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-22964632-C-A
• chr2-22964632-C-G

Variant summary

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

The ENST00000723051.1(ENSG00000294349):​n.97+37103G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,904 control chromosomes in the GnomAD database, including 28,481 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 0.61 (28481 hom., cov: 33)
• Consequence: ENSG00000294349 ENST00000723051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 11 publications found

Genes affected

ENSG00000294349 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723051.1. 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
	ENSG00000294349	ENST00000723051.1		n.97+37103G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91980 AN: 151784 Hom.: 28451 Cov.: 33

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.606 AC: 92066 AN: 151904 Hom.: 28481 Cov.: 33 AF XY: 0.608 AC XY: 45143 AN XY: 74218

African (AFR) AF: 0.717 AC: 29752 AN: 41470

American (AMR) AF: 0.618 AC: 9428 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1979 AN: 3470

East Asian (EAS) AF: 0.711 AC: 3679 AN: 5176

South Asian (SAS) AF: 0.679 AC: 3266 AN: 4810

European-Finnish (FIN) AF: 0.516 AC: 5433 AN: 10522

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.539 AC: 36624 AN: 67886

Other (OTH) AF: 0.616 AC: 1302 AN: 2112

Alfa AF: 0.568 Hom.: 96665

Bravo AF: 0.616

Asia WGS AF: 0.702 AC: 2439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.21
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs2681019; hg19: chr2-23187504;