chr6-29827156-A-G

Variant names:

• chr6-29827156-A-G
• rs2735022
• NM_001363567.2:c.6+112A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001363567.2(HLA-G):​c.6+112A>G 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 466,350 control chromosomes in the GnomAD database, including 59,998 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 0.49 (18128 hom., cov: 32)
  • Exomes 𝑓: 0.50 (41870 hom.)
• Consequence: HLA-G NM_001363567.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 15 publications found

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-F-AS1 (HGNC:26645): (HLA-F antisense RNA 1)

HCG4P8 (HGNC:22927): (HLA complex group 4 pseudogene 8)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• 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 rank	MANE	Protein	UniProt
HLA-G	NM_001363567.2	c.6+112A>G		intron_variant	Intron 1 of 7		NP_001350496.1
HLA-G	NM_001384280.1	c.6+112A>G		intron_variant	Intron 2 of 8		NP_001371209.1
HLA-G	NM_002127.6	c.-113+112A>G		intron_variant	Intron 1 of 7		NP_002118.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-G	ENST00000376828.6	c.6+112A>G		intron_variant	Intron 1 of 7	6		ENSP00000366024.2
HLA-G	ENST00000428701.6	n.66+112A>G		intron_variant	Intron 1 of 4	6
HLA-F-AS1	ENST00000849927.1	n.26+1315T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73688 AN: 151908 Hom.: 18105 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.500

GnomAD4 exome AF: 0.504 AC: 158567 AN: 314324 Hom.: 41870 AF XY: 0.524 AC XY: 93056 AN XY: 177582

African (AFR) AF: 0.515 AC: 4342 AN: 8434

American (AMR) AF: 0.504 AC: 13567 AN: 26904

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 6091 AN: 10640

East Asian (EAS) AF: 0.607 AC: 5582 AN: 9202

South Asian (SAS) AF: 0.670 AC: 39820 AN: 59450

European-Finnish (FIN) AF: 0.342 AC: 8787 AN: 25706

Middle Eastern (MID) AF: 0.537 AC: 1412 AN: 2630

European-Non Finnish (NFE) AF: 0.457 AC: 71869 AN: 157200

Other (OTH) AF: 0.501 AC: 7097 AN: 14158

GnomAD4 genome AF: 0.485 AC: 73752 AN: 152026 Hom.: 18128 Cov.: 32 AF XY: 0.485 AC XY: 36042 AN XY: 74294

African (AFR) AF: 0.510 AC: 21119 AN: 41420

American (AMR) AF: 0.514 AC: 7855 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1967 AN: 3468

East Asian (EAS) AF: 0.611 AC: 3159 AN: 5172

South Asian (SAS) AF: 0.666 AC: 3218 AN: 4830

European-Finnish (FIN) AF: 0.340 AC: 3594 AN: 10562

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31183 AN: 67988

Other (OTH) AF: 0.506 AC: 1064 AN: 2104

Alfa AF: 0.428 Hom.: 3426

Bravo AF: 0.496

Asia WGS AF: 0.685 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.48
PhyloP100		-1.2
PromoterAI		-0.0078	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2735022; hg19: chr6-29794933;