6-29975492-G-A

Variant names:

• chr6-29975492-G-A
• rs1128306
• ENST00000376800.7:n.381G>A

Variant summary

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

The ENST00000376800.7(HCG9):​n.381G>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 ENST00000376800.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• Publications: 12 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]

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

POLR1HASP (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HCG9	NR_028032.1	n.378G>A		non_coding_transcript_exon_variant	Exon 1 of 3
MICD		n.29975492G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG9	ENST00000376800.7	n.381G>A		non_coding_transcript_exon_variant	Exon 1 of 3	1
POLR1HASP	ENST00000849678.1	n.589-28576C>T		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1	n.65+1111C>T		intron_variant	Intron 1 of 5

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

African (AFR) AF: 0.324 AC: 1758 AN: 5432

American (AMR) AF: 0.277 AC: 3391 AN: 12220

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 915 AN: 4836

East Asian (EAS) AF: 0.164 AC: 1396 AN: 8508

South Asian (SAS) AF: 0.233 AC: 10363 AN: 44496

European-Finnish (FIN) AF: 0.131 AC: 3151 AN: 24020

Middle Eastern (MID) AF: 0.199 AC: 156 AN: 784

European-Non Finnish (NFE) AF: 0.150 AC: 17887 AN: 118918

Other (OTH) AF: 0.173 AC: 1783 AN: 10282

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

African (AFR) AF: 0.330 AC: 13647 AN: 41308

American (AMR) AF: 0.277 AC: 4230 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3470

East Asian (EAS) AF: 0.139 AC: 719 AN: 5160

South Asian (SAS) AF: 0.238 AC: 1145 AN: 4806

European-Finnish (FIN) AF: 0.126 AC: 1329 AN: 10580

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.160 AC: 10845 AN: 67940

Other (OTH) AF: 0.238 AC: 503 AN: 2110

Alfa AF: 0.232 Hom.: 1141

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

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