chr6-31826815-C-T

Variant names:

• chr6-31826815-C-T
• rs2763979
• ENST00000700791.2:n.629G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000700791.2(ENSG00000289829):​n.629G>A variant causes a non coding transcript exon 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 ENST00000700791.2 non_coding_transcript_exon
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -2.06
• Publications: 87 publications found

Genes affected

ENSG00000289829 (HGNC:):

SNHG32 (HGNC:19078): (small nucleolar RNA host gene 32) Predicted to enable double-stranded RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000700791.2	n.629G>A		non_coding_transcript_exon_variant	Exon 1 of 1
SNHG32	ENST00000718216.1	n.209-388C>T		intron_variant	Intron 1 of 4
SNHG32	ENST00000718219.1	n.184+4514C>T		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.653 AC: 27023 AN: 41406

American (AMR) AF: 0.440 AC: 6694 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1077 AN: 3458

East Asian (EAS) AF: 0.285 AC: 1473 AN: 5170

South Asian (SAS) AF: 0.402 AC: 1933 AN: 4810

European-Finnish (FIN) AF: 0.452 AC: 4773 AN: 10550

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.349 AC: 23684 AN: 67894

Other (OTH) AF: 0.459 AC: 963 AN: 2100

Alfa AF: 0.381 Hom.: 43074

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2763979; hg19: chr6-31794592;