rs2244579

Variant names:

• chr6-31468862-G-C
• rs2244579
• ENST00000414046.3:n.5602G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-31468862-G-C
• chr6-31468862-G-T

Variant summary

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

The ENST00000414046.3(HCP5):​n.5602G>C 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 0.303 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 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.816
• Publications: 16 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=-0.93).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000414046.3	n.5602G>C		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000467369.2	n.217+5354G>C		intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2	n.95+5583G>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.414 AC: 17055 AN: 41162

American (AMR) AF: 0.285 AC: 4334 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1715 AN: 3466

East Asian (EAS) AF: 0.306 AC: 1574 AN: 5142

South Asian (SAS) AF: 0.252 AC: 1212 AN: 4810

European-Finnish (FIN) AF: 0.180 AC: 1902 AN: 10586

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.252 AC: 17131 AN: 67972

Other (OTH) AF: 0.344 AC: 719 AN: 2092

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
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs2244579; hg19: chr6-31436639;