6-31468270-T-C

Position:

• chr6-31468270-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414046.3(HCP5):​n.5010T>C 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 0.714 in 151,670 control chromosomes in the GnomAD database, including 39,115 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 0.71 (39115 hom., cov: 31)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

Genes affected

HCP5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31468270T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000414046.3	n.5010T>C		non_coding_transcript_exon_variant	2/2	4
HCP5	ENST00000467369.2	n.217+4762T>C		intron_variant		4
HCP5	ENST00000666495.2	n.95+4991T>C		intron_variant
HCP5	ENST00000674016.1	n.97+4140T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108217 AN: 151552 Hom.: 39084 Cov.: 31

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.756

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.714 AC: 108298 AN: 151670 Hom.: 39115 Cov.: 31 AF XY: 0.721 AC XY: 53465 AN XY: 74134

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.758

Alfa AF: 0.676 Hom.: 14868

Bravo AF: 0.722

Asia WGS AF: 0.793 AC: 2759 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.66
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2518028; hg19: chr6-31436047;