6-29872039-T-C

Variant names:

• chr6-29872039-T-C
• rs3094654
• ENST00000630472.1:n.1745A>G

Variant summary

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

The ENST00000630472.1(HCP5B):​n.1745A>G 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 0.623 in 152,160 control chromosomes in the GnomAD database, including 29,634 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 (29619 hom., cov: 33)
  • Exomes 𝑓: 0.66 (15 hom.)
• Consequence: HCP5B ENST00000630472.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 12 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=-0.95).
• 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.1745A>G		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.1745A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000290870	ENST00000647952.1	n.2062+11515A>G		intron_variant	Intron 1 of 3
POLR1HASP	ENST00000849679.1	n.587-9213A>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94589 AN: 151972 Hom.: 29581 Cov.: 33

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.624

GnomAD4 exome AF: 0.662 AC: 45 AN: 68 Hom.: 15 Cov.: 0 AF XY: 0.604 AC XY: 29 AN XY: 48

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

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

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.696 AC: 32 AN: 46

Other (OTH) AF: 0.750 AC: 6 AN: 8

GnomAD4 genome AF: 0.622 AC: 94677 AN: 152092 Hom.: 29619 Cov.: 33 AF XY: 0.615 AC XY: 45748 AN XY: 74352

African (AFR) AF: 0.631 AC: 26181 AN: 41462

American (AMR) AF: 0.617 AC: 9429 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2293 AN: 3472

East Asian (EAS) AF: 0.465 AC: 2408 AN: 5178

South Asian (SAS) AF: 0.528 AC: 2543 AN: 4820

European-Finnish (FIN) AF: 0.545 AC: 5774 AN: 10588

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

European-Non Finnish (NFE) AF: 0.647 AC: 43982 AN: 67974

Other (OTH) AF: 0.619 AC: 1307 AN: 2110

Alfa AF: 0.641 Hom.: 72142

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	-0.95
CADD	Benign	4.4
DANN	Benign	0.43
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs3094654; hg19: chr6-29839816;