6-31470817-C-T

Position:

• chr6-31470817-C-T

Variant summary

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

The ENST00000414046.3(HCP5):​n.7557C>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 0.786 in 151,716 control chromosomes in the GnomAD database, including 47,336 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 0.79 (47336 hom., cov: 31)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

Genes affected

HCP5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31470817C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000414046.3	n.7557C>T		non_coding_transcript_exon_variant	2/2	4
HCP5	ENST00000467369.2	n.218-6210C>T		intron_variant		4
HCP5	ENST00000666495.2	n.96-6210C>T		intron_variant
HCP5	ENST00000674016.1	n.98-6210C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119139 AN: 151598 Hom.: 47270 Cov.: 31

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.779

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.786 AC: 119266 AN: 151716 Hom.: 47336 Cov.: 31 AF XY: 0.786 AC XY: 58339 AN XY: 74180

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.802

Alfa AF: 0.744 Hom.: 11102

Bravo AF: 0.799

Asia WGS AF: 0.811 AC: 2821 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.099

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523666; hg19: chr6-31438594;