chr6-31468056-C-G

Variant names:

• chr6-31468056-C-G
• rs2244546
• ENST00000414046.3:n.4796C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414046.3(HCP5):​n.4796C>G 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 0.0788 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 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 35 publications found

Genes affected

HCP5 (HGNC:21659): (HLA complex P5)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000414046.3	n.4796C>G		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000467369.2	n.217+4548C>G		intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2	n.95+4777C>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.0174 AC: 721 AN: 41326

American (AMR) AF: 0.147 AC: 2234 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.0499 AC: 173 AN: 3464

East Asian (EAS) AF: 0.104 AC: 539 AN: 5162

South Asian (SAS) AF: 0.0589 AC: 284 AN: 4820

European-Finnish (FIN) AF: 0.144 AC: 1522 AN: 10566

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0930 AC: 6322 AN: 67990

Other (OTH) AF: 0.0697 AC: 147 AN: 2110

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
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs2244546; hg19: chr6-31435833;