rs2523676

chr6-31468214-C-T

Variant summary

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

The ENST00000666495.2(HCP5):n.95+4935C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 151,818 control chromosomes in the GnomAD database, including 2,398 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 0.16 (2398 hom., cov: 32)
• Consequence: HCP5 ENST00000666495.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCP5	ENST00000666495.2	n.95+4935C>T		intron_variant, non_coding_transcript_variant
HCP5	ENST00000414046.3	n.4954C>T		non_coding_transcript_exon_variant	2/2	4
HCP5	ENST00000467369.2	n.217+4706C>T		intron_variant, non_coding_transcript_variant		4
HCP5	ENST00000674016.1	n.97+4084C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24349 AN: 151700 Hom.: 2393 Cov.: 32

Gnomad AFR AF: 0.0998

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.0560

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.161 AC: 24371 AN: 151818 Hom.: 2398 Cov.: 32 AF XY: 0.162 AC XY: 12029 AN XY: 74196

Gnomad4 AFR AF: 0.0999

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.0560

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.128

Alfa AF: 0.167 Hom.: 802

Bravo AF: 0.160

Asia WGS AF: 0.168 AC: 586 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.8
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523676; hg19: chr6-31435991;