rs2940695

Variant names:

• chr13-107914807-G-A
• rs2940695
• ENST00000663056.1:n.105-18221G>A

Variant summary

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

The ENST00000663056.1(ENSG00000286343):​n.105-18221G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,900 control chromosomes in the GnomAD database, including 10,266 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 0.36 (10266 hom., cov: 31)
• Consequence: ENSG00000286343 ENST00000663056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.845
• Publications: 1 publications found

Genes affected

ENSG00000286343 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 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
ENSG00000286343	ENST00000663056.1	n.105-18221G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54562 AN: 151784 Hom.: 10269 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.359 AC: 54572 AN: 151900 Hom.: 10266 Cov.: 31 AF XY: 0.356 AC XY: 26421 AN XY: 74228

African (AFR) AF: 0.256 AC: 10600 AN: 41404

American (AMR) AF: 0.438 AC: 6679 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1405 AN: 3464

East Asian (EAS) AF: 0.214 AC: 1103 AN: 5156

South Asian (SAS) AF: 0.385 AC: 1853 AN: 4810

European-Finnish (FIN) AF: 0.305 AC: 3214 AN: 10544

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28322 AN: 67940

Other (OTH) AF: 0.381 AC: 804 AN: 2112

Alfa AF: 0.401 Hom.: 10961

Bravo AF: 0.360

Asia WGS AF: 0.320 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.2
DANN	Benign	0.73
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs2940695; hg19: chr13-108567155;