rs1736933

Positions:

• chr6-29827359-A-C

Variant summary

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

The NM_001363567.2(HLA-G):​c.6+315A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 351,580 control chromosomes in the GnomAD database, including 44,938 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 (18027 hom., cov: 31)
  • Exomes 𝑓: 0.51 (26911 hom.)
• Consequence: HLA-G NM_001363567.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

HLA-G (HGNC:4964): (major histocompatibility complex, class I, G) HLA-G belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. HLA-G is expressed on fetal derived placental cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domain, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exon 6 encodes the cytoplasmic tail. [provided by RefSeq, Jul 2008]

HLA-G (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-G	NM_001363567.2	c.6+315A>C		intron_variant			NP_001350496.1
HLA-G	NM_001384280.1	c.6+315A>C		intron_variant			NP_001371209.1
HLA-G	NM_002127.6	c.-113+315A>C		intron_variant			NP_002118.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-G	ENST00000376828.6	c.6+315A>C		intron_variant		6		ENSP00000366024.2
HLA-G	ENST00000428701.6	n.66+315A>C		intron_variant		6
HCG4P8	ENST00000443049.1	n.*26T>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73465 AN: 151530 Hom.: 18004 Cov.: 31

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.501

GnomAD4 exome AF: 0.507 AC: 101388 AN: 199932 Hom.: 26911 Cov.: 0 AF XY: 0.529 AC XY: 58373 AN XY: 110420

Gnomad4 AFR exome AF: 0.506

Gnomad4 AMR exome AF: 0.509

Gnomad4 ASJ exome AF: 0.574

Gnomad4 EAS exome AF: 0.604

Gnomad4 SAS exome AF: 0.668

Gnomad4 FIN exome AF: 0.365

Gnomad4 NFE exome AF: 0.453

Gnomad4 OTH exome AF: 0.490

GnomAD4 genome AF: 0.485 AC: 73529 AN: 151648 Hom.: 18027 Cov.: 31 AF XY: 0.485 AC XY: 35920 AN XY: 74112

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.507

Alfa AF: 0.472 Hom.: 2096

Bravo AF: 0.497

Asia WGS AF: 0.684 AC: 2381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1736933; hg19: chr6-29795136; COSMIC: COSV64407033; COSMIC: COSV64407033;