rs1886166

Variant names:

• chr13-37616450-A-T
• rs1886166
• ENST00000744989.1:n.49-11576A>T

Variant summary

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

The ENST00000744989.1(ENSG00000297050):​n.49-11576A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,008 control chromosomes in the GnomAD database, including 6,992 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 0.29 (6992 hom., cov: 32)
• Consequence: ENSG00000297050 ENST00000744989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• Publications: 1 publications found

Genes affected

ENSG00000297050 (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 = 0.348 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
ENSG00000297050	ENST00000744989.1	n.49-11576A>T		intron_variant	Intron 1 of 4
ENSG00000297050	ENST00000744990.1	n.71-11576A>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44638 AN: 151890 Hom.: 6982 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.294 AC: 44665 AN: 152008 Hom.: 6992 Cov.: 32 AF XY: 0.285 AC XY: 21184 AN XY: 74306

African (AFR) AF: 0.206 AC: 8548 AN: 41494

American (AMR) AF: 0.291 AC: 4435 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1709 AN: 3468

East Asian (EAS) AF: 0.161 AC: 831 AN: 5174

South Asian (SAS) AF: 0.336 AC: 1619 AN: 4824

European-Finnish (FIN) AF: 0.253 AC: 2668 AN: 10566

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23870 AN: 67916

Other (OTH) AF: 0.312 AC: 657 AN: 2106

Alfa AF: 0.324 Hom.: 1039

Bravo AF: 0.294

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.88
DANN	Benign	0.73
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1886166; hg19: chr13-38190587; COSMIC: COSV69347296;