chr6-29792813-G-T

Variant names:

• chr6-29792813-G-T
• rs1611213
• ENST00000446817.1:n.559G>T

Variant summary

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

The NR_002139.2(HCG4):​n.261C>A 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 0.00000111 in 897,380 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: 31)
  • Exomes 𝑓: 0.0000011 (0 hom.)
• Consequence: HCG4 NR_002139.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 0 publications found

Genes affected

HLA-V (HGNC:):

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

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

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

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=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_002139.2. 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.261C>A		non_coding_transcript_exon	Exon 1 of 1
	HLA-V	NR_132323.1		n.670+107G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-V	ENST00000446817.1	TSL:6	n.559G>T		non_coding_transcript_exon	Exon 4 of 4
	HLA-F-AS1	ENST00000849876.1		n.89C>A		non_coding_transcript_exon	Exon 1 of 2
	HLA-F-AS1	ENST00000849921.1		n.109C>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000111 AC: 1 AN: 897380 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 432978

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 16800

American (AMR) AF: 0.00 AC: 0 AN: 10440

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8296

East Asian (EAS) AF: 0.00 AC: 0 AN: 10942

South Asian (SAS) AF: 0.0000183 AC: 1 AN: 54712

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 11808

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3290

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 748482

Other (OTH) AF: 0.00 AC: 0 AN: 32610

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.84
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1611213; hg19: chr6-29760590;