rs2244579

chr6-31468862-G-Cchr6-31468862-G-T

Variant summary

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

The ENST00000666495.2(HCP5):n.95+5583G>C 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 0.303 in 151,638 control chromosomes in the GnomAD database, including 7,888 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 0.30 (7888 hom., cov: 33)
• Consequence: HCP5 ENST00000666495.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.816

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 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+5583G>C		intron_variant, non_coding_transcript_variant
HCP5	ENST00000414046.3	n.5602G>C		non_coding_transcript_exon_variant	2/2	4
HCP5	ENST00000467369.2	n.217+5354G>C		intron_variant, non_coding_transcript_variant		4
HCP5	ENST00000674016.1	n.97+4732G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45853 AN: 151522 Hom.: 7880 Cov.: 33

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.303 AC: 45886 AN: 151638 Hom.: 7888 Cov.: 33 AF XY: 0.296 AC XY: 21956 AN XY: 74140

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.344

Alfa AF: 0.282 Hom.: 856

Bravo AF: 0.319

Asia WGS AF: 0.340 AC: 1180 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.4
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2244579; hg19: chr6-31436639;