rs1736935

Variant names:

• chr6-29826666-A-G
• rs1736935

Your query was ambiguous. Multiple possible variants found:

• chr6-29826666-A-G
• chr6-29826666-A-T

Variant summary

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

The variant allele was found at a frequency of 0.543 in 151,988 control chromosomes in the GnomAD database, including 22,823 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 0.54 (22823 hom., cov: 32)
• Consequence: HCG4P8 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 19 publications found

Genes affected

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

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)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG4P8		n.29826666A>G		intragenic_variant
HLA-G	NM_001384280.1	c.-37+119A>G		intron_variant	Intron 1 of 8		NP_001371209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-F-AS1	ENST00000849927.1	n.26+1805T>C		intron_variant	Intron 1 of 3
HLA-F-AS1	ENST00000849935.1	n.230+1054T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82434 AN: 151870 Hom.: 22789 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.543 AC: 82517 AN: 151988 Hom.: 22823 Cov.: 32 AF XY: 0.540 AC XY: 40137 AN XY: 74300

African (AFR) AF: 0.614 AC: 25415 AN: 41416

American (AMR) AF: 0.600 AC: 9165 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2234 AN: 3464

East Asian (EAS) AF: 0.618 AC: 3182 AN: 5152

South Asian (SAS) AF: 0.694 AC: 3348 AN: 4826

European-Finnish (FIN) AF: 0.350 AC: 3698 AN: 10566

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33636 AN: 67972

Other (OTH) AF: 0.577 AC: 1217 AN: 2110

Alfa AF: 0.534 Hom.: 7740

Bravo AF: 0.563

Asia WGS AF: 0.710 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.58
PhyloP100		-1.8
PromoterAI		-0.0024	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1736935; hg19: chr6-29794443;