chr6-29826540-G-A

Position:

• chr6-29826540-G-A

Variant summary

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

The NM_001384280.1(HLA-G):​c.-44G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,868 control chromosomes in the GnomAD database, including 17,930 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 0.48 (17930 hom., cov: 31)
• Consequence: HLA-G NM_001384280.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702

Genes affected

HLA-G (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLA-G	NM_001384280.1	c.-44G>A		5_prime_UTR_variant	1/9

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73252 AN: 151750 Hom.: 17914 Cov.: 31

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.483 AC: 73306 AN: 151868 Hom.: 17930 Cov.: 31 AF XY: 0.482 AC XY: 35812 AN XY: 74222

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.502

Alfa AF: 0.479 Hom.: 24166

Bravo AF: 0.493

Asia WGS AF: 0.678 AC: 2360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.52
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1736936; hg19: chr6-29794317; COSMIC: COSV64407025;