ENST00000418983.1:n.101T>C

Variant names:

• chr6-29792650-A-G
• rs751493222
• ENST00000418983.1:n.101T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000418983.1(HCG4):​n.101T>C 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 0.000000809 in 1,236,714 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 8.1e-7 (0 hom.)
• Consequence: HCG4 ENST00000418983.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• Publications: 0 publications found

Genes affected

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

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

HLA-V (HGNC:):

HLA-F-AS1 (HGNC:26645): (HLA-F antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418983.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG4	NR_002139.2		n.424T>C		non_coding_transcript_exon	Exon 1 of 1
	HLA-V	NR_132323.1		n.614A>G		non_coding_transcript_exon	Exon 2 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG4	ENST00000418983.1	TSL:6	n.101T>C		non_coding_transcript_exon	Exon 1 of 1
	HLA-V	ENST00000429037.2	TSL:6	n.286A>G		non_coding_transcript_exon	Exon 2 of 3
	HLA-V	ENST00000446817.1	TSL:6	n.396A>G		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000512 AC: 1 AN: 195202 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 8.09e-7 AC: 1 AN: 1236714 Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0 AN XY: 610652

African (AFR) AF: 0.00 AC: 0 AN: 26446

American (AMR) AF: 0.00 AC: 0 AN: 33952

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18040

East Asian (EAS) AF: 0.00 AC: 0 AN: 19990

South Asian (SAS) AF: 0.0000125 AC: 1 AN: 80096

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32664

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4692

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 974138

Other (OTH) AF: 0.00 AC: 0 AN: 46696

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.37
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs751493222; hg19: chr6-29760427;