rs2244546

Positions:

• chr6-31468056-C-G

Variant summary

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

The ENST00000666495.2(HCP5):​n.95+4777C>G 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 0.0788 in 151,850 control chromosomes in the GnomAD database, including 733 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 0.079 (733 hom., cov: 32)
• Consequence: HCP5 ENST00000666495.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.142 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+4777C>G		intron_variant, non_coding_transcript_variant
HCP5	ENST00000414046.3	n.4796C>G		non_coding_transcript_exon_variant	2/2	4
HCP5	ENST00000467369.2	n.217+4548C>G		intron_variant, non_coding_transcript_variant		4
HCP5	ENST00000674016.1	n.97+3926C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0788 AC: 11952 AN: 151730 Hom.: 727 Cov.: 32

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0788 AC: 11968 AN: 151850 Hom.: 733 Cov.: 32 AF XY: 0.0827 AC XY: 6137 AN XY: 74250

Gnomad4 AFR AF: 0.0174

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0589

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.0930

Gnomad4 OTH AF: 0.0697

Alfa AF: 0.0852 Hom.: 388

Bravo AF: 0.0759

Asia WGS AF: 0.0850 AC: 297 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2244546; hg19: chr6-31435833;