rs13147758

chr4-144539078-A-G

Variant summary

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

The XR_939273.3(LOC105377462):n.164+22906T>C variant causes a intron, non coding transcript 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: LOC105377462 XR_939273.3 intron, non_coding_transcript
• Clinical Significance: association no assertion criteria provided O:2
• Conservation: PhyloP100: 1.53

Genes affected

LOC105377462 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105377462	XR_939273.3	n.164+22906T>C		intron_variant, non_coding_transcript_variant
LOC105377462	XR_939272.3	n.164+22906T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.0950

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.303

Alfa AF: 0.387 Hom.: 14479

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

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 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	8.8
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13147758; hg19: chr4-145460230;