2-189553964-C-T

Variant names:

• chr2-189553964-C-T
• rs12693541
• ENST00000838943.1:n.37+3518G>A

Variant summary

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

The ENST00000838943.1(ENSG00000309131):​n.37+3518G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,108 control chromosomes in the GnomAD database, including 43,673 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 0.73 (43673 hom., cov: 32)
• Consequence: ENSG00000309131 ENST00000838943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.695
• Publications: 8 publications found

Genes affected

ENSG00000309131 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.864 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
ENSG00000309131	ENST00000838943.1	n.37+3518G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110549 AN: 151990 Hom.: 43687 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.727 AC: 110541 AN: 152108 Hom.: 43673 Cov.: 32 AF XY: 0.732 AC XY: 54457 AN XY: 74358

African (AFR) AF: 0.388 AC: 16094 AN: 41474

American (AMR) AF: 0.804 AC: 12286 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2949 AN: 3472

East Asian (EAS) AF: 0.840 AC: 4346 AN: 5176

South Asian (SAS) AF: 0.781 AC: 3763 AN: 4816

European-Finnish (FIN) AF: 0.890 AC: 9427 AN: 10588

Middle Eastern (MID) AF: 0.771 AC: 225 AN: 292

European-Non Finnish (NFE) AF: 0.870 AC: 59137 AN: 67990

Other (OTH) AF: 0.733 AC: 1549 AN: 2112

Alfa AF: 0.790 Hom.: 17864

Bravo AF: 0.705

Asia WGS AF: 0.770 AC: 2675 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.41
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs12693541; hg19: chr2-190418690;