rs1348864

Variant names:

• chr2-22959390-A-C
• rs1348864
• ENST00000723051.1:n.97+42345T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-22959390-A-C
• chr2-22959390-A-T

Variant summary

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

The ENST00000723051.1(ENSG00000294349):​n.97+42345T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,028 control chromosomes in the GnomAD database, including 34,215 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 0.67 (34215 hom., cov: 32)
• Consequence: ENSG00000294349 ENST00000723051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 4 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 = 0.69 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
ENSG00000294349	ENST00000723051.1	n.97+42345T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101397 AN: 151910 Hom.: 34173 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.668 AC: 101490 AN: 152028 Hom.: 34215 Cov.: 32 AF XY: 0.665 AC XY: 49393 AN XY: 74288

African (AFR) AF: 0.697 AC: 28895 AN: 41452

American (AMR) AF: 0.619 AC: 9453 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2196 AN: 3466

East Asian (EAS) AF: 0.369 AC: 1901 AN: 5150

South Asian (SAS) AF: 0.637 AC: 3061 AN: 4808

European-Finnish (FIN) AF: 0.729 AC: 7713 AN: 10576

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46001 AN: 67984

Other (OTH) AF: 0.657 AC: 1389 AN: 2114

Alfa AF: 0.665 Hom.: 103876

Bravo AF: 0.657

Asia WGS AF: 0.500 AC: 1742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1348864; hg19: chr2-23182262;