rs1828591

Positions:

• chr4-144559628-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+2356T>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 0.428 in 152,006 control chromosomes in the GnomAD database, including 14,210 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.43 (14210 hom., cov: 32)
• Consequence: LOC105377462 XR_939273.3 intron, non_coding_transcript
• Clinical Significance: association no assertion criteria provided O:2
• Conservation: PhyloP100: -0.420

Genes affected

LOC105377462 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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	UniProt
LOC105377462	XR_939273.3	n.164+2356T>C		intron_variant, non_coding_transcript_variant
LOC105377462	XR_939272.3	n.164+2356T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64965 AN: 151888 Hom.: 14197 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.428 AC: 65008 AN: 152006 Hom.: 14210 Cov.: 32 AF XY: 0.432 AC XY: 32078 AN XY: 74296

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.379

Alfa AF: 0.411 Hom.: 20385

Bravo AF: 0.408

Asia WGS AF: 0.382 AC: 1331 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 08, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1828591; hg19: chr4-145480780;