6-31464348-C-T

Position:

• chr6-31464348-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

HCP5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
HCP5	NR_040662.1	n.1078C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000541196.3	n.339C>T		non_coding_transcript_exon_variant	4/4	1
HCP5	ENST00000414046.3	n.1088C>T		non_coding_transcript_exon_variant	2/2	4
HCP5	ENST00000670109.1	n.1051C>T		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR exome AF: 0.313

Gnomad4 AMR exome AF: 0.333

Gnomad4 ASJ exome AF: 0.667

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.552

Gnomad4 FIN exome AF: 0.368

Gnomad4 NFE exome AF: 0.415

Gnomad4 OTH exome AF: 0.448

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

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.477

Alfa AF: 0.477 Hom.: 31907

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2284178; hg19: chr6-31432125;