rs2031836

Variant names:

• chr13-109386243-G-A
• rs2031836
• ENST00000750929.1:n.111+14461C>T

Variant summary

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

The ENST00000750929.1(ENSG00000297783):​n.111+14461C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,080 control chromosomes in the GnomAD database, including 12,052 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 0.38 (12052 hom., cov: 33)
• Consequence: ENSG00000297783 ENST00000750929.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 4 publications found

Genes affected

ENSG00000297783 (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 (NFE) allele frequency at 95% confidence interval = 0.469 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
ENSG00000297783	ENST00000750929.1	n.111+14461C>T		intron_variant	Intron 1 of 1
ENSG00000297807	ENST00000751145.1	n.815-3402G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57871 AN: 151964 Hom.: 12049 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.381 AC: 57892 AN: 152080 Hom.: 12052 Cov.: 33 AF XY: 0.378 AC XY: 28098 AN XY: 74336

African (AFR) AF: 0.203 AC: 8420 AN: 41502

American (AMR) AF: 0.410 AC: 6258 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3470

East Asian (EAS) AF: 0.413 AC: 2136 AN: 5168

South Asian (SAS) AF: 0.315 AC: 1518 AN: 4820

European-Finnish (FIN) AF: 0.429 AC: 4532 AN: 10570

Middle Eastern (MID) AF: 0.321 AC: 93 AN: 290

European-Non Finnish (NFE) AF: 0.474 AC: 32194 AN: 67960

Other (OTH) AF: 0.384 AC: 812 AN: 2112

Alfa AF: 0.440 Hom.: 48588

Bravo AF: 0.374

Asia WGS AF: 0.356 AC: 1238 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	1.6
DANN	Benign	0.75
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2031836; hg19: chr13-110038590;