2-226183055-C-T

Variant names:

• chr2-226183055-C-T
• rs2943653
• ENST00000423838.2:n.333-1930G>A

Variant summary

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

The ENST00000423838.2(ENSG00000235070):​n.333-1930G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,880 control chromosomes in the GnomAD database, including 31,715 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 0.64 (31715 hom., cov: 31)
• Consequence: ENSG00000235070 ENST00000423838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 18 publications found

Genes affected

ENSG00000235070 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 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
ENSG00000235070	ENST00000423838.2	n.333-1930G>A		intron_variant	Intron 1 of 1	1
ENSG00000235070	ENST00000719962.1	n.93+2265G>A		intron_variant	Intron 1 of 1
ENSG00000235070	ENST00000719964.1	n.299+2265G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96967 AN: 151762 Hom.: 31687 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.639 AC: 97030 AN: 151880 Hom.: 31715 Cov.: 31 AF XY: 0.641 AC XY: 47566 AN XY: 74196

African (AFR) AF: 0.502 AC: 20795 AN: 41388

American (AMR) AF: 0.732 AC: 11168 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2591 AN: 3468

East Asian (EAS) AF: 0.905 AC: 4662 AN: 5152

South Asian (SAS) AF: 0.779 AC: 3752 AN: 4818

European-Finnish (FIN) AF: 0.651 AC: 6861 AN: 10532

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45088 AN: 67948

Other (OTH) AF: 0.656 AC: 1385 AN: 2110

Alfa AF: 0.648 Hom.: 6503

Bravo AF: 0.639

Asia WGS AF: 0.833 AC: 2896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.30
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2943653; hg19: chr2-227047771;