rs3129791

chr6-28986516-G-A

Variant summary

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

The NR_135289.2(HCG15):n.237-161G>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 0.0514 in 154,206 control chromosomes in the GnomAD database, including 337 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 0.052 (336 hom., cov: 32)
  • Exomes 𝑓: 0.0041 (1 hom.)
• Consequence: HCG15 NR_135289.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

Genes affected

HCG15 (HGNC:18361): (HLA complex group 15)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG15	NR_135289.2	n.237-161G>A		intron_variant, non_coding_transcript_variant
HCG15	NR_145490.1	n.422+10G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG15	ENST00000438190.1	n.224+10G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0521 AC: 7929 AN: 152152 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0246

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0403

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0901

Gnomad OTH AF: 0.0344

GnomAD4 exome AF: 0.00413 AC: 8 AN: 1936 Hom.: 1 Cov.: 0 AF XY: 0.00302 AC XY: 3 AN XY: 994

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00270

Gnomad4 NFE exome AF: 0.0517

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0520 AC: 7925 AN: 152270 Hom.: 336 Cov.: 32 AF XY: 0.0464 AC XY: 3452 AN XY: 74450

Gnomad4 AFR AF: 0.0174

Gnomad4 AMR AF: 0.0245

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.0403

Gnomad4 NFE AF: 0.0901

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0797 Hom.: 593

Bravo AF: 0.0500

Asia WGS AF: 0.00404 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.9
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129791; hg19: chr6-28954293;