dbSNP rs1611213: HLA-V:n.559G>A (chr6-29792813-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_002139.2(HCG4):n.261C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 1,040,490 control chromosomes in the GnomAD database, including 62,705 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 0.39 ( 12368 hom., cov: 31)

Exomes 𝑓: 0.33 ( 50337 hom. )

Consequence

HCG4
NR_002139.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.349

Variant links:

Genes affected

HLA-V (HGNC:):

HLA-V links:

HCG4 (HGNC:21241): (HLA complex group 4)

HCG4 links:

HLA-V (HGNC:23482): (major histocompatibility complex, class I, V (pseudogene))

HLA-V links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG4	NR_002139.2 link	n.261C>T		non_coding_transcript_exon_variant	Exon 1 of 1
HLA-V	NR_132323.1 link	n.670+107G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HLA-V	ENST00000446817.1 link	n.559G>A	non_coding_transcript_exon_variant	Exon 4 of 4	6
HLA-V	ENST00000429037.2 link	n.342+107G>A	intron_variant	Intron 2 of 2	6
HLA-V	ENST00000457107.5 link	n.353+107G>A	intron_variant	Intron 2 of 2	6

Frequencies

GnomAD3 genomes

AF:

0.389

AC:

59058

AN:

151684

Hom.:

12353

Cov.:

show subpopulations

Gnomad AFR

AF:

0.544

Gnomad AMI

AF:

0.205

Gnomad AMR

AF:

0.385

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.199

Gnomad SAS

AF:

0.352

Gnomad FIN

AF:

0.206

Gnomad MID

AF:

0.490

Gnomad NFE

AF:

0.340

Gnomad OTH

AF:

0.402

GnomAD4 exome

AF:

0.332

AC:

294974

AN:

888688

Hom.:

50337

Cov.:

AF XY:

0.334

AC XY:

143026

AN XY:

428744

show subpopulations

Gnomad4 AFR exome

AF:

0.525

Gnomad4 AMR exome

AF:

0.299

Gnomad4 ASJ exome

AF:

0.426

Gnomad4 EAS exome

AF:

0.159

Gnomad4 SAS exome

AF:

0.371

Gnomad4 FIN exome

AF:

0.208

Gnomad4 NFE exome

AF:

0.328

Gnomad4 OTH exome

AF:

0.334

GnomAD4 genome

AF:

0.389

AC:

59107

AN:

151802

Hom.:

12368

Cov.:

AF XY:

0.381

AC XY:

28253

AN XY:

74194

show subpopulations

Gnomad4 AFR

AF:

0.543

Gnomad4 AMR

AF:

0.385

Gnomad4 ASJ

AF:

0.459

Gnomad4 EAS

AF:

0.199

Gnomad4 SAS

AF:

0.353

Gnomad4 FIN

AF:

0.206

Gnomad4 NFE

AF:

0.340

Gnomad4 OTH

AF:

0.397

Alfa

AF:

0.366

Hom.:

2436

Bravo

AF:

0.413

Asia WGS

AF:

0.280

AC:

976

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

DANN

Benign

0.93

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over