chr6-29790748-T-C

Variant names:

• chr6-29790748-T-C
• rs1610640
• ENST00000446817.1:n.-206T>C

Variant summary

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

The ENST00000446817.1(HLA-V):​n.-206T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,150 control chromosomes in the GnomAD database, including 13,506 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 0.41 (13506 hom., cov: 33)
• Consequence: HLA-V ENST00000446817.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

HLA-V (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 (AFR) allele frequency at 95% confidence interval = 0.562 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-V	ENST00000446817.1	n.-206T>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61571 AN: 152032 Hom.: 13484 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.405 AC: 61631 AN: 152150 Hom.: 13506 Cov.: 33 AF XY: 0.396 AC XY: 29452 AN XY: 74376

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.424

Alfa AF: 0.408 Hom.: 1199

Bravo AF: 0.431

Asia WGS AF: 0.288 AC: 1004 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	5.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1610640; hg19: chr6-29758525;