6-31470817-C-T

Variant names:

• chr6-31470817-C-T
• rs2523666
• ENST00000414046.3:n.7557C>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:21659): (HLA complex P5)

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 rank	MANE	Protein	UniProt

Ensembl

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

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;