rs13118928

Variant names:

• chr4-144565237-A-G
• rs13118928
• ENST00000649263.1:n.328-149259T>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-149259T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,158 control chromosomes in the GnomAD database, including 9,707 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.33 (9707 hom., cov: 33)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: association no assertion criteria provided O:2
• Conservation: PhyloP100: 0.0910
• Publications: 59 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 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
ENSG00000285713	ENST00000649263.1	n.328-149259T>C		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-149259T>C		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50180 AN: 152040 Hom.: 9697 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.330 AC: 50196 AN: 152158 Hom.: 9707 Cov.: 33 AF XY: 0.337 AC XY: 25056 AN XY: 74378

African (AFR) AF: 0.134 AC: 5552 AN: 41554

American (AMR) AF: 0.308 AC: 4709 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1552 AN: 5168

South Asian (SAS) AF: 0.492 AC: 2375 AN: 4826

European-Finnish (FIN) AF: 0.537 AC: 5673 AN: 10566

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 28038 AN: 67988

Other (OTH) AF: 0.309 AC: 653 AN: 2110

Alfa AF: 0.386 Hom.: 39971

Bravo AF: 0.296

Asia WGS AF: 0.363 AC: 1264 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:2

Revision: no assertion criteria provided

Submissions by phenotype

Chronic obstructive pulmonary disease, biomass related Other:1

Feb 12, 2020

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Significance: association

Review Status: no assertion criteria provided

Collection Method: case-control

- -

Chronic obstructive pulmonary disease Other:1

Dec 07, 2019

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Significance: association

Review Status: no assertion criteria provided

Collection Method: case-control

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.2
DANN	Benign	0.60
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs13118928; hg19: chr4-145486389;