rs1611213

chr6-29792813-G-Achr6-29792813-G-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

Genes affected

HCG4 (HGNC:):

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

ACMG classification

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/exons	MANE	UniProt
HCG4	NR_002139.2	n.261C>T		non_coding_transcript_exon_variant	1/1
HLA-V	NR_132323.1	n.670+107G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-V	ENST00000429037.2	n.342+107G>A		intron_variant, non_coding_transcript_variant
HLA-V	ENST00000476601.5	n.670+107G>A		intron_variant, non_coding_transcript_variant
HLA-V	ENST00000446817.1	n.559G>A		non_coding_transcript_exon_variant	4/4
HLA-V	ENST00000457107.5	n.353+107G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59058 AN: 151684 Hom.: 12353 Cov.: 31

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.: 12 AF XY: 0.334 AC XY: 143026 AN XY: 428744

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.: 31 AF XY: 0.381 AC XY: 28253 AN XY: 74194

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	13
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1611213; hg19: chr6-29760590; COSMIC: COSV57641536;