rs7745002

Positions:

• chr6-32647644-A-G
• chr6-32647644-A-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.613+5391A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,648 control chromosomes in the GnomAD database, including 15,089 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 0.44 (15089 hom., cov: 31)
• Consequence: HLA-DQA1 XM_006715079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.02

Genes affected

HLA-DQA1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-DQA1	XM_006715079.5	c.613+5391A>G		intron_variant			XP_006715142.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67101 AN: 151530 Hom.: 15085 Cov.: 31

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.443 AC: 67138 AN: 151648 Hom.: 15089 Cov.: 31 AF XY: 0.443 AC XY: 32781 AN XY: 74062

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.422

Alfa AF: 0.439 Hom.: 1855

Bravo AF: 0.454

Asia WGS AF: 0.384 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7745002; hg19: chr6-32615421;