rs2243621

chr6-31464043-C-T

Variant summary

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

The ENST00000541196.3(HCP5):n.198-10C>T variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 434,120 control chromosomes in the GnomAD database, including 9,709 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 0.21 (4010 hom., cov: 32)
  • Exomes 𝑓: 0.18 (5699 hom.)
• Consequence: HCP5 ENST00000541196.3 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCP5	NR_040662.1	n.773C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCP5	ENST00000666495.2	n.95+764C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31892 AN: 151568 Hom.: 4001 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.0900

Gnomad EAS AF: 0.0655

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.206

GnomAD3 exomes AF: 0.194 AC: 34517 AN: 177968 Hom.: 4186 AF XY: 0.187 AC XY: 17975 AN XY: 96068

Gnomad AFR exome AF: 0.298

Gnomad AMR exome AF: 0.276

Gnomad ASJ exome AF: 0.105

Gnomad EAS exome AF: 0.0581

Gnomad SAS exome AF: 0.110

Gnomad FIN exome AF: 0.317

Gnomad NFE exome AF: 0.174

Gnomad OTH exome AF: 0.175

GnomAD4 exome AF: 0.181 AC: 51037 AN: 282434 Hom.: 5699 Cov.: 0 AF XY: 0.171 AC XY: 27490 AN XY: 160624

Gnomad4 AFR exome AF: 0.295

Gnomad4 AMR exome AF: 0.273

Gnomad4 ASJ exome AF: 0.101

Gnomad4 EAS exome AF: 0.0721

Gnomad4 SAS exome AF: 0.110

Gnomad4 FIN exome AF: 0.303

Gnomad4 NFE exome AF: 0.172

Gnomad4 OTH exome AF: 0.169

GnomAD4 genome AF: 0.211 AC: 31955 AN: 151686 Hom.: 4010 Cov.: 32 AF XY: 0.216 AC XY: 15984 AN XY: 74144

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.0900

Gnomad4 EAS AF: 0.0659

Gnomad4 SAS AF: 0.0960

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.204

Alfa AF: 0.178 Hom.: 1587

Bravo AF: 0.208

Asia WGS AF: 0.108 AC: 374 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.6
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243621; hg19: chr6-31431820; COSMIC: COSV69993674;