ENST00000630472.1:n.1179G>A

Variant names:

• chr6-29872605-C-T
• rs9258966
• ENST00000630472.1:n.1179G>A

Variant summary

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

The ENST00000630472.1(HCP5B):​n.1179G>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 0.622 in 152,450 control chromosomes in the GnomAD database, including 29,662 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 0.62 (29587 hom., cov: 31)
  • Exomes 𝑓: 0.57 (75 hom.)
• Consequence: HCP5B ENST00000630472.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776
• Publications: 14 publications found

Genes affected

HCP5B (HGNC:30984): (HLA complex P5B)

ENSG00000290870 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCP5B	NR_031762.2	n.1179G>A		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCP5B	ENST00000630472.1	n.1179G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000290870	ENST00000647952.1	n.2062+10949G>A		intron_variant	Intron 1 of 3
POLR1HASP	ENST00000849679.1	n.587-9779G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94488 AN: 151856 Hom.: 29550 Cov.: 31

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.624

GnomAD4 exome AF: 0.565 AC: 268 AN: 474 Hom.: 75 Cov.: 0 AF XY: 0.594 AC XY: 171 AN XY: 288

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.547 AC: 233 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.694 AC: 25 AN: 36

Other (OTH) AF: 0.800 AC: 8 AN: 10

GnomAD4 genome AF: 0.622 AC: 94574 AN: 151976 Hom.: 29587 Cov.: 31 AF XY: 0.615 AC XY: 45691 AN XY: 74270

African (AFR) AF: 0.631 AC: 26148 AN: 41434

American (AMR) AF: 0.617 AC: 9438 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2286 AN: 3464

East Asian (EAS) AF: 0.463 AC: 2386 AN: 5154

South Asian (SAS) AF: 0.526 AC: 2533 AN: 4812

European-Finnish (FIN) AF: 0.545 AC: 5756 AN: 10564

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43957 AN: 67934

Other (OTH) AF: 0.619 AC: 1310 AN: 2116

Alfa AF: 0.639 Hom.: 31431

Bravo AF: 0.631

Asia WGS AF: 0.458 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.13
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs9258966; hg19: chr6-29840382;