rs3129791

Variant names:

• chr6-28986516-G-A
• rs3129791
• ENST00000759771.1:n.298G>A

Variant summary

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

The ENST00000759771.1(HCG15):​n.298G>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 0.0514 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 ENST00000759771.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 32 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HCG15	NR_135289.2	n.237-161G>A		intron_variant	Intron 1 of 2
HCG15	NR_145490.1	n.422+10G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG15	ENST00000759771.1	n.298G>A		non_coding_transcript_exon_variant	Exon 3 of 5
HCG15	ENST00000759779.1	n.423G>A		non_coding_transcript_exon_variant	Exon 3 of 5
HCG15	ENST00000438190.1	n.224+10G>A		intron_variant	Intron 2 of 2	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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00270 AC: 5 AN: 1854

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0517 AC: 3 AN: 58

Other (OTH) AF: 0.00 AC: 0 AN: 20

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

African (AFR) AF: 0.0174 AC: 722 AN: 41554

American (AMR) AF: 0.0245 AC: 375 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 72 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4824

European-Finnish (FIN) AF: 0.0403 AC: 428 AN: 10608

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0901 AC: 6127 AN: 68012

Other (OTH) AF: 0.0341 AC: 72 AN: 2112

Alfa AF: 0.0769 Hom.: 1244

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
PhyloP100		-0.076
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs3129791; hg19: chr6-28954293;