rs17843604

chr6-32652506-C-T

Variant summary

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

The XM_006715079.5(HLA-DQA1):c.614-2161C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 147,426 control chromosomes in the GnomAD database, including 18,842 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 0.50 (18842 hom., cov: 26)
• Consequence: HLA-DQA1 XM_006715079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.860

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 = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLA-DQA1	XM_006715079.5	c.614-2161C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.496 AC: 73082 AN: 147314 Hom.: 18841 Cov.: 26

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.681

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.496 AC: 73126 AN: 147426 Hom.: 18842 Cov.: 26 AF XY: 0.488 AC XY: 35008 AN XY: 71810

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.521

Alfa AF: 0.563 Hom.: 25192

Bravo AF: 0.517

Asia WGS AF: 0.401 AC: 1396 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	0.23
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17843604; hg19: chr6-32620283; COSMIC: COSV68419671;