rs1128306

Positions:

• chr6-29975492-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_028032.1(HCG9):​n.378G>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 0.194 in 381,338 control chromosomes in the GnomAD database, including 8,199 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 0.22 (4154 hom., cov: 30)
  • Exomes 𝑓: 0.18 (4045 hom.)
• Consequence: HCG9 NR_028032.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HCG9	NR_028032.1	n.378G>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCG9	ENST00000376800.7	n.381G>A		non_coding_transcript_exon_variant	1/3	1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33188 AN: 151724 Hom.: 4136 Cov.: 30

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.241

GnomAD4 exome AF: 0.178 AC: 40800 AN: 229496 Hom.: 4045 Cov.: 0 AF XY: 0.184 AC XY: 23308 AN XY: 126882

Gnomad4 AFR exome AF: 0.324

Gnomad4 AMR exome AF: 0.277

Gnomad4 ASJ exome AF: 0.189

Gnomad4 EAS exome AF: 0.164

Gnomad4 SAS exome AF: 0.233

Gnomad4 FIN exome AF: 0.131

Gnomad4 NFE exome AF: 0.150

Gnomad4 OTH exome AF: 0.173

GnomAD4 genome AF: 0.219 AC: 33257 AN: 151842 Hom.: 4154 Cov.: 30 AF XY: 0.217 AC XY: 16136 AN XY: 74208

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.238

Alfa AF: 0.180 Hom.: 402

Bravo AF: 0.238

Asia WGS AF: 0.186 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1128306; hg19: chr6-29943269; COSMIC: COSV65136142;