6-31464348-C-T

Variant names:

• chr6-31464348-C-T
• rs2284178
• ENST00000541196.3:n.339C>T

Variant summary

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

The ENST00000541196.3(HCP5):​n.339C>T 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 0.448 in 155,894 control chromosomes in the GnomAD database, including 16,315 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 0.45 (15873 hom., cov: 33)
  • Exomes 𝑓: 0.45 (442 hom.)
• Consequence: HCP5 ENST00000541196.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179
• Publications: 44 publications found

Genes affected

HCP5 (HGNC:21659): (HLA complex P5)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCP5	NR_040662.1	n.1078C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000541196.3	n.339C>T		non_coding_transcript_exon_variant	Exon 4 of 4	1
HCP5	ENST00000414046.3	n.1088C>T		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000670109.1	n.1051C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68014 AN: 151660 Hom.: 15868 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.472

GnomAD4 exome AF: 0.454 AC: 1868 AN: 4116 Hom.: 442 Cov.: 0 AF XY: 0.470 AC XY: 1058 AN XY: 2252

African (AFR) AF: 0.313 AC: 5 AN: 16

American (AMR) AF: 0.333 AC: 8 AN: 24

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 56 AN: 84

East Asian (EAS) AF: 0.750 AC: 3 AN: 4

South Asian (SAS) AF: 0.552 AC: 551 AN: 998

European-Finnish (FIN) AF: 0.368 AC: 95 AN: 258

Middle Eastern (MID) AF: 0.679 AC: 19 AN: 28

European-Non Finnish (NFE) AF: 0.415 AC: 1020 AN: 2456

Other (OTH) AF: 0.448 AC: 111 AN: 248

GnomAD4 genome AF: 0.448 AC: 68045 AN: 151778 Hom.: 15873 Cov.: 33 AF XY: 0.446 AC XY: 33094 AN XY: 74180

African (AFR) AF: 0.371 AC: 15309 AN: 41294

American (AMR) AF: 0.473 AC: 7201 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2502 AN: 3468

East Asian (EAS) AF: 0.533 AC: 2733 AN: 5130

South Asian (SAS) AF: 0.531 AC: 2553 AN: 4806

European-Finnish (FIN) AF: 0.370 AC: 3915 AN: 10588

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32239 AN: 67966

Other (OTH) AF: 0.477 AC: 1005 AN: 2108

Alfa AF: 0.468 Hom.: 72236

Bravo AF: 0.454

Asia WGS AF: 0.538 AC: 1874 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.2
DANN	Benign	0.88
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2284178; hg19: chr6-31432125;