Variant rs6904029 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_028032.1(HCG9):n.176G>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
NR_028032.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.655

Variant links:

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]

HCG9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	UniProt
HCG9	NR_028032.1 linkuse as main transcript	n.176G>A		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39696

AN:

151628

Hom.:

5502

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.272

AC XY:

58234

AN XY:

214172

show subpopulations

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.:

AF XY:

0.261

AC XY:

19354

AN XY:

74112

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over