rs400488

Variant names:

• chr6-29975258-G-A
• rs400488
• ENST00000376800.7:n.147G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-29975258-G-A
• chr6-29975258-G-C
• chr6-29975258-G-T

Variant summary

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

The ENST00000376800.7(HCG9):​n.147G>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 ENST00000376800.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 29 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000376800.7. 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.144G>A		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG9	ENST00000376800.7	TSL:1	n.147G>A		non_coding_transcript_exon	Exon 1 of 3
	POLR1HASP	ENST00000849678.1		n.589-28342C>T		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+1345C>T		intron	N/A

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

GnomAD2 exomes AF: 0.186 AC: 44828 AN: 240778 AF XY: 0.182

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 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

African (AFR) AF: 0.322 AC: 3386 AN: 10502

American (AMR) AF: 0.277 AC: 9870 AN: 35586

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 2244 AN: 11714

East Asian (EAS) AF: 0.175 AC: 2322 AN: 13302

South Asian (SAS) AF: 0.229 AC: 15171 AN: 66176

European-Finnish (FIN) AF: 0.129 AC: 4041 AN: 31306

Middle Eastern (MID) AF: 0.193 AC: 550 AN: 2846

European-Non Finnish (NFE) AF: 0.150 AC: 28706 AN: 191936

Other (OTH) AF: 0.182 AC: 3041 AN: 16696

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

African (AFR) AF: 0.331 AC: 13682 AN: 41342

American (AMR) AF: 0.278 AC: 4247 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3468

East Asian (EAS) AF: 0.142 AC: 730 AN: 5126

South Asian (SAS) AF: 0.239 AC: 1151 AN: 4816

European-Finnish (FIN) AF: 0.126 AC: 1330 AN: 10580

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

European-Non Finnish (NFE) AF: 0.160 AC: 10858 AN: 67920

Other (OTH) AF: 0.244 AC: 514 AN: 2110

Alfa AF: 0.185 Hom.: 10230

Bravo AF: 0.238

Asia WGS AF: 0.216 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.1
DANN	Benign	0.60
PhyloP100		-0.32

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: rs400488;

hg19: chr6-29943035;

COSMIC: COSV65136404;