rs13118928

Positions:

• chr4-144565237-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: association no assertion criteria provided O:2
• Conservation: PhyloP100: 0.0910

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.309

Alfa AF: 0.394 Hom.: 18948

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

association, no assertion criteria provided

case-control

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Feb 12, 2020

- -

Chronic obstructive pulmonary disease Other:1

association, no assertion criteria provided

case-control

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Dec 07, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13118928; hg19: chr4-145486389;