rs13147758

Variant names:

• chr4-144539078-A-G
• rs13147758
• ENST00000649263.1:n.328-123100T>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-123100T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,120 control chromosomes in the GnomAD database, including 9,456 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.32 (9456 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: association no assertion criteria provided O:2
• Conservation: PhyloP100: 1.53
• Publications: 42 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.164+22906T>C		intron_variant	Intron 1 of 7
LOC105377462	XR_939273.3	n.164+22906T>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-123100T>C		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-123100T>C		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48459 AN: 152000 Hom.: 9447 Cov.: 32

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.319 AC: 48474 AN: 152120 Hom.: 9456 Cov.: 32 AF XY: 0.326 AC XY: 24220 AN XY: 74334

African (AFR) AF: 0.0950 AC: 3948 AN: 41538

American (AMR) AF: 0.311 AC: 4748 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1140 AN: 3472

East Asian (EAS) AF: 0.301 AC: 1551 AN: 5160

South Asian (SAS) AF: 0.491 AC: 2366 AN: 4822

European-Finnish (FIN) AF: 0.536 AC: 5655 AN: 10544

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.411 AC: 27962 AN: 67984

Other (OTH) AF: 0.303 AC: 640 AN: 2112

Alfa AF: 0.382 Hom.: 36268

Bravo AF: 0.285

Asia WGS AF: 0.359 AC: 1250 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 06, 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	-0.87
CADD	Benign	8.8
DANN	Benign	0.35
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs13147758; hg19: chr4-145460230;