rs2763979

Positions:

• chr6-31826815-C-T

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 0.448 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: intergenic_region
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -2.06

Genes affected

(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/exons	MANE	Protein	UniProt
		n.31826815C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

association, no assertion criteria provided

case-control

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Aug 04, 2019

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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;