rs1008438

chr6-31815431-A-Cchr6-31815431-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.429 in 596,576 control chromosomes in the GnomAD database, including 59,283 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency:
  • Genomes: 𝑓 0.51 (21347 hom., cov: 31)
  • Exomes 𝑓: 0.40 (37936 hom.)
• Consequence: Unknown
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.162

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76984 AN: 151764 Hom.: 21320 Cov.: 31

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.516

GnomAD4 exome AF: 0.402 AC: 178819 AN: 444694 Hom.: 37936 Cov.: 4 AF XY: 0.401 AC XY: 94639 AN XY: 235736

Gnomad4 AFR exome AF: 0.740

Gnomad4 AMR exome AF: 0.474

Gnomad4 ASJ exome AF: 0.381

Gnomad4 EAS exome AF: 0.411

Gnomad4 SAS exome AF: 0.459

Gnomad4 FIN exome AF: 0.475

Gnomad4 NFE exome AF: 0.363

Gnomad4 OTH exome AF: 0.434

GnomAD4 genome AF: 0.507 AC: 77056 AN: 151882 Hom.: 21347 Cov.: 31 AF XY: 0.509 AC XY: 37810 AN XY: 74226

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.517

Alfa AF: 0.255 Hom.: 512

Bravo AF: 0.518

Asia WGS AF: 0.550 AC: 1910 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	-0.33
Cadd	Benign	11
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1008438; hg19: chr6-31783208;