chr6-29978172-G-T

Variant names:

• chr6-29978172-G-T
• rs3132685
• ENST00000376800.7:n.471-46G>T

Variant summary

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

The ENST00000850532.1(HCG9):​n.889G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.038 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HCG9 ENST00000850532.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 33 publications found

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]

POLR1HASP (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850532.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG9	NR_028032.1		n.468-46G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG9	ENST00000376800.7	TSL:1	n.471-46G>T		intron	N/A
	HCG9	ENST00000463275.2	TSL:5	n.1370G>T		non_coding_transcript_exon	Exon 2 of 2
	HCG9	ENST00000850532.1		n.889G>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0376 AC: 4984 AN: 132504 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0871

Gnomad AMI AF: 0.00111

Gnomad AMR AF: 0.0502

Gnomad ASJ AF: 0.0400

Gnomad EAS AF: 0.0531

Gnomad SAS AF: 0.0526

Gnomad FIN AF: 0.00486

Gnomad MID AF: 0.0568

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0445

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0377 AC: 4999 AN: 132602 Hom.: 0 Cov.: 33 AF XY: 0.0377 AC XY: 2454 AN XY: 65120

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

African (AFR) AF: 0.0871 AC: 2776 AN: 31884

American (AMR) AF: 0.0504 AC: 648 AN: 12856

Ashkenazi Jewish (ASJ) AF: 0.0400 AC: 118 AN: 2950

East Asian (EAS) AF: 0.0534 AC: 230 AN: 4306

South Asian (SAS) AF: 0.0534 AC: 213 AN: 3988

European-Finnish (FIN) AF: 0.00486 AC: 50 AN: 10290

Middle Eastern (MID) AF: 0.0569 AC: 14 AN: 246

European-Non Finnish (NFE) AF: 0.0137 AC: 869 AN: 63388

Other (OTH) AF: 0.0445 AC: 80 AN: 1796

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.000231 Hom.: 3736

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.029
DANN	Benign	0.53
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs3132685; hg19: chr6-29945949; COSMIC: COSV65136353;