6-29873295-C-T

Variant names:

• chr6-29873295-C-T
• rs1611650
• ENST00000630472.1:n.489G>A

Variant summary

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

The ENST00000630472.1(HCP5B):​n.489G>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 0.109 in 152,266 control chromosomes in the GnomAD database, including 999 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 0.11 (998 hom., cov: 33)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: HCP5B ENST00000630472.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.982
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCP5B	NR_031762.2	n.489G>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.489G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000290870	ENST00000647952.1	n.2062+10259G>A		intron_variant	Intron 1 of 3
POLR1HASP	ENST00000849679.1	n.587-10469G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16547 AN: 152106 Hom.: 992 Cov.: 33

Gnomad AFR AF: 0.0790

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0553

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.132

GnomAD4 exome AF: 0.119 AC: 5 AN: 42 Hom.: 1 Cov.: 0 AF XY: 0.156 AC XY: 5 AN XY: 32

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

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

European-Non Finnish (NFE) AF: 0.156 AC: 5 AN: 32

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.109 AC: 16588 AN: 152224 Hom.: 998 Cov.: 33 AF XY: 0.109 AC XY: 8077 AN XY: 74414

African (AFR) AF: 0.0797 AC: 3310 AN: 41554

American (AMR) AF: 0.133 AC: 2027 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 868 AN: 3460

East Asian (EAS) AF: 0.0554 AC: 287 AN: 5178

South Asian (SAS) AF: 0.106 AC: 510 AN: 4826

European-Finnish (FIN) AF: 0.0758 AC: 804 AN: 10604

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8369 AN: 68000

Other (OTH) AF: 0.130 AC: 274 AN: 2104

Alfa AF: 0.0555 Hom.: 76

Bravo AF: 0.111

Asia WGS AF: 0.0740 AC: 259 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	4.7
DANN	Benign	0.49
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs1611650; hg19: chr6-29841072;