rs1736935

chr6-29826666-A-Gchr6-29826666-A-T

Variant summary

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

The NM_001384280.1(HLA-G):c.-37+119A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: HLA-G NM_001384280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

Genes affected

HLA-G (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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/exons	MANE	UniProt
HLA-G	NM_001384280.1	c.-37+119A>G		intron_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.577

Alfa AF: 0.518 Hom.: 3761

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1736935; hg19: chr6-29794443;