6-29872039-T-C

Position:

• chr6-29872039-T-C

Variant summary

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

The NR_031762.2(HCP5B):​n.1745A>G 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 0.623 in 152,160 control chromosomes in the GnomAD database, including 29,634 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 0.62 (29619 hom., cov: 33)
  • Exomes 𝑓: 0.66 (15 hom.)
• Consequence: HCP5B NR_031762.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

Genes affected

HCP5B (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 (NFE) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCP5B	NR_031762.2	n.1745A>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCP5B	ENST00000630472.1	n.1745A>G		non_coding_transcript_exon_variant	1/1
	ENST00000647952.1	n.2062+11515A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94589 AN: 151972 Hom.: 29581 Cov.: 33

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.624

GnomAD4 exome AF: 0.662 AC: 45 AN: 68 Hom.: 15 Cov.: 0 AF XY: 0.604 AC XY: 29 AN XY: 48

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.696

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.622 AC: 94677 AN: 152092 Hom.: 29619 Cov.: 33 AF XY: 0.615 AC XY: 45748 AN XY: 74352

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.619

Alfa AF: 0.644 Hom.: 40163

Bravo AF: 0.631

Asia WGS AF: 0.458 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094654; hg19: chr6-29839816;