rs400488

chr6-29975258-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.144G>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 0.193 in 531,894 control chromosomes in the GnomAD database, including 11,249 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 (4183 hom., cov: 30)
  • Exomes 𝑓: 0.18 (7066 hom.)
• Consequence: HCG9 NR_028032.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

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=-0.83).
• 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	UniProt
HCG9	NR_028032.1	n.144G>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG9	ENST00000376800.7	n.147G>A		non_coding_transcript_exon_variant	1/3	1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33277 AN: 151712 Hom.: 4164 Cov.: 30

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.243

GnomAD3 exomes AF: 0.186 AC: 44828 AN: 240778 Hom.: 4635 AF XY: 0.182 AC XY: 23893 AN XY: 131212

Gnomad AFR exome AF: 0.317

Gnomad AMR exome AF: 0.276

Gnomad ASJ exome AF: 0.190

Gnomad EAS exome AF: 0.160

Gnomad SAS exome AF: 0.217

Gnomad FIN exome AF: 0.125

Gnomad NFE exome AF: 0.149

Gnomad OTH exome AF: 0.187

GnomAD4 exome AF: 0.182 AC: 69331 AN: 380064 Hom.: 7066 Cov.: 0 AF XY: 0.184 AC XY: 39770 AN XY: 216256

Gnomad4 AFR exome AF: 0.322

Gnomad4 AMR exome AF: 0.277

Gnomad4 ASJ exome AF: 0.192

Gnomad4 EAS exome AF: 0.175

Gnomad4 SAS exome AF: 0.229

Gnomad4 FIN exome AF: 0.129

Gnomad4 NFE exome AF: 0.150

Gnomad4 OTH exome AF: 0.182

GnomAD4 genome AF: 0.220 AC: 33352 AN: 151830 Hom.: 4183 Cov.: 30 AF XY: 0.218 AC XY: 16169 AN XY: 74200

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.244

Alfa AF: 0.175 Hom.: 3483

Bravo AF: 0.238

Asia WGS AF: 0.216 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.1
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs400488; hg19: chr6-29943035; COSMIC: COSV65136404;