rs2763979

Variant names:

• chr6-31826815-C-T
• rs2763979
• ENST00000700791.1:n.*26G>A

Variant summary

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

The ENST00000700791.1(ENSG00000289829):​n.*26G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,806 control chromosomes in the GnomAD database, including 16,793 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.45 (16793 hom., cov: 32)
• Consequence: ENSG00000289829 ENST00000700791.1 downstream_gene
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -2.06

Genes affected

ENSG00000289829 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 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
ENSG00000289829	ENST00000700791.1	n.*26G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67887 AN: 151688 Hom.: 16766 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.448 AC: 67961 AN: 151806 Hom.: 16793 Cov.: 32 AF XY: 0.448 AC XY: 33231 AN XY: 74178

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.459

Alfa AF: 0.360 Hom.: 16756

Bravo AF: 0.456

Asia WGS AF: 0.463 AC: 1608 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Chronic obstructive pulmonary disease Other:1

Aug 04, 2019

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Significance: association

Review Status: no assertion criteria provided

Collection Method: case-control

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.3
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2763979; hg19: chr6-31794592;