ENST00000425174.1:n.-238A>C

Variant names:

• chr6-31382526-T-G
• rs2844535
• ENST00000425174.1:n.-238A>C

Variant summary

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

The ENST00000425174.1(HLA-S):​n.-238A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,958 control chromosomes in the GnomAD database, including 6,239 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 0.28 (6239 hom., cov: 31)
• Consequence: HLA-S ENST00000425174.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

Genes affected

HLA-S (HGNC:19395): (major histocompatibility complex, class I, S (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-S	ENST00000425174.1	n.-238A>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43060 AN: 151840 Hom.: 6228 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.284 AC: 43117 AN: 151958 Hom.: 6239 Cov.: 31 AF XY: 0.284 AC XY: 21072 AN XY: 74284

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.270

Alfa AF: 0.153 Hom.: 300

Bravo AF: 0.281

Asia WGS AF: 0.239 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844535; hg19: chr6-31350303;