rs3132685

Positions:

• chr6-29978172-G-A
• chr6-29978172-G-T

Variant summary

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

The NR_028032.1(HCG9):​n.468-46G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0644 in 151,338 control chromosomes in the GnomAD database, including 504 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 0.064 (504 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HCG9 NR_028032.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

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]

POLR1HASP (HGNC:13924): (POLR1H antisense, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG9	NR_028032.1	n.468-46G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG9	ENST00000376800.7	n.471-46G>A		intron_variant, non_coding_transcript_variant		1
POLR1HASP	ENST00000688495.1	n.361-777C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9747 AN: 151226 Hom.: 504 Cov.: 33

Gnomad AFR AF: 0.0164

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0267

Gnomad ASJ AF: 0.0316

Gnomad EAS AF: 0.000968

Gnomad SAS AF: 0.00461

Gnomad FIN AF: 0.0636

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0414

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0644 AC: 9742 AN: 151338 Hom.: 504 Cov.: 33 AF XY: 0.0587 AC XY: 4341 AN XY: 73976

Gnomad4 AFR AF: 0.0164

Gnomad4 AMR AF: 0.0266

Gnomad4 ASJ AF: 0.0316

Gnomad4 EAS AF: 0.000970

Gnomad4 SAS AF: 0.00440

Gnomad4 FIN AF: 0.0636

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0410

Alfa AF: 0.0975 Hom.: 1500

Bravo AF: 0.0596

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.073
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132685; hg19: chr6-29945949;