chr6-29978172-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000850532.1(HCG9):​n.889G>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 0.0644 in 151,338 control chromosomes in the GnomAD database, including 504 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 0.064 (504 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

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

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9747 AN: 151226 Hom.: 504 Cov.: 33

Gnomad AFR AF: 0.0164

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0267

Gnomad ASJ AF: 0.0316

Gnomad EAS AF: 0.000968

Gnomad SAS AF: 0.00461

Gnomad FIN AF: 0.0636

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0414

GnomAD4 exome Data not reliable, filtered out with message: AC0 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 AF: 0.0644 AC: 9742 AN: 151338 Hom.: 504 Cov.: 33 AF XY: 0.0587 AC XY: 4341 AN XY: 73976

African (AFR) AF: 0.0164 AC: 673 AN: 41070

American (AMR) AF: 0.0266 AC: 404 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0316 AC: 109 AN: 3450

East Asian (EAS) AF: 0.000970 AC: 5 AN: 5152

South Asian (SAS) AF: 0.00440 AC: 21 AN: 4768

European-Finnish (FIN) AF: 0.0636 AC: 672 AN: 10560

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.113 AC: 7636 AN: 67818

Other (OTH) AF: 0.0410 AC: 86 AN: 2100

Alfa AF: 0.0976 Hom.: 3736

Bravo AF: 0.0596

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.073
DANN	Benign	0.78
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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.

Other links and lift over

dbSNP: rs3132685;

hg19: chr6-29945949;