Genetic Variant HCG9:n.179G>C (chr6-29975290-G-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000376800.7(HCG9):n.179G>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 0.00000531 in 376,744 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: 30)

Exomes 𝑓: 0.0000053 ( 0 hom. )

Consequence

HCG9
ENST00000376800.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.655

Publications

0 publications found

Variant links:

Genes affected

HCG9 (HGNC:21243): (HLA complex group 9) This gene lies within the MHC class I region on chromosome 6p21.3. This gene is believed to be non-coding, but its function has not been determined. [provided by RefSeq, Jul 2009]

HCG9 links:

MICD (HGNC:7093): (MHC class I polypeptide-related sequence D (pseudogene))

MICD links:

POLR1HASP (HGNC:):

POLR1HASP links:

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new If you want to explore the variant's impact on the transcript ENST00000376800.7, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000376800.7. 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
	HCG9	NR_028032.1		n.176G>C		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
HCG9	ENST00000376800.7	TSL:1	n.179G>C	non_coding_transcript_exon	Exon 1 of 3
POLR1HASP	ENST00000849678.1		n.589-28374C>G	intron	N/A
POLR1HASP	ENST00000849679.1		n.65+1313C>G	intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000531

AC:

AN:

376744

Hom.:

Cov.:

AF XY:

0.00000933

AC XY:

AN XY:

214266

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10494

American (AMR)

AF:

0.00

AC:

AN:

34800

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11628

East Asian (EAS)

AF:

0.00

AC:

AN:

13352

South Asian (SAS)

AF:

0.00

AC:

AN:

65554

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31148

Middle Eastern (MID)

AF:

0.000703

AC:

AN:

2846

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

190326

Other (OTH)

AF:

0.00

AC:

AN:

16596

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.8

(source)

DANN

Benign

0.66

PhyloP100

0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over