rs6904029

Positions:

• chr6-29975290-G-A

Variant summary

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

The ENST00000376800.7(HCG9):​n.179G>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 0.277 in 528,338 control chromosomes in the GnomAD database, including 21,577 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 0.26 (5502 hom., cov: 30)
  • Exomes 𝑓: 0.28 (16075 hom.)
• Consequence: HCG9 ENST00000376800.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.655

Genes affected

HCG9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HCG9	NR_028032.1	n.176G>A		non_coding_transcript_exon_variant	1/3
MICD		n.29975290G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCG9	ENST00000376800.7	n.179G>A		non_coding_transcript_exon_variant	1/3	1

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39696 AN: 151628 Hom.: 5502 Cov.: 30

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.240

GnomAD3 exomes AF: 0.291 AC: 67287 AN: 231422 Hom.: 10192 AF XY: 0.284 AC XY: 35799 AN XY: 126082

Gnomad AFR exome AF: 0.204

Gnomad AMR exome AF: 0.330

Gnomad ASJ exome AF: 0.195

Gnomad EAS exome AF: 0.329

Gnomad SAS exome AF: 0.175

Gnomad FIN exome AF: 0.371

Gnomad NFE exome AF: 0.310

Gnomad OTH exome AF: 0.272

GnomAD4 exome AF: 0.283 AC: 106465 AN: 376592 Hom.: 16075 Cov.: 0 AF XY: 0.272 AC XY: 58234 AN XY: 214172

Gnomad4 AFR exome AF: 0.200

Gnomad4 AMR exome AF: 0.326

Gnomad4 ASJ exome AF: 0.193

Gnomad4 EAS exome AF: 0.322

Gnomad4 SAS exome AF: 0.176

Gnomad4 FIN exome AF: 0.366

Gnomad4 NFE exome AF: 0.306

Gnomad4 OTH exome AF: 0.276

GnomAD4 genome AF: 0.262 AC: 39692 AN: 151746 Hom.: 5502 Cov.: 30 AF XY: 0.261 AC XY: 19354 AN XY: 74112

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.237

Alfa AF: 0.283 Hom.: 12350

Bravo AF: 0.255

Asia WGS AF: 0.200 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6904029; hg19: chr6-29943067; COSMIC: COSV65136300;