6-31472305-C-T

Position:

• chr6-31472305-C-T

Variant summary

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

The ENST00000414046.3(HCP5):​n.9045C>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 0.403 in 151,722 control chromosomes in the GnomAD database, including 13,520 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 0.40 (13520 hom., cov: 33)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

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 (AFR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HCG26	NR_002812.3	n.1077C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000414046.3	n.9045C>T		non_coding_transcript_exon_variant	2/2	4
HCP5	ENST00000467369.2	n.218-4722C>T		intron_variant		4
HCP5	ENST00000666495.2	n.96-4722C>T		intron_variant
HCP5	ENST00000674016.1	n.98-4722C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61075 AN: 151604 Hom.: 13493 Cov.: 33

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.403 AC: 61148 AN: 151722 Hom.: 13520 Cov.: 33 AF XY: 0.401 AC XY: 29762 AN XY: 74154

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.435

Alfa AF: 0.348 Hom.: 16639

Bravo AF: 0.411

Asia WGS AF: 0.402 AC: 1400 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	7.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1055569; hg19: chr6-31440082;