6-32647933-G-C

Variant summary

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

The XM_006715079.5(HLA-DQA1):c.613+5680G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 150,236 control chromosomes in the GnomAD database, including 24,694 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.57 (24694 hom., cov: 30)
• Consequence: HLA-DQA1 XM_006715079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

HLA-DQA1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLA-DQA1	XM_006715079.5	c.613+5680G>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.568 AC: 85334 AN: 150114 Hom.: 24685 Cov.: 30

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.714

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.568 AC: 85392 AN: 150236 Hom.: 24694 Cov.: 30 AF XY: 0.565 AC XY: 41447 AN XY: 73320

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.582

Alfa AF: 0.448 Hom.: 1158

Bravo AF: 0.584

Asia WGS AF: 0.486 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.30
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17612633; hg19: chr6-32615710;