rs17206855

Variant names:

• chr6-31463762-T-C
• rs17206855
• ENST00000541196.3:n.197+254T>C

Variant summary

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

The ENST00000541196.3(HCP5):​n.197+254T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0194 in 434,256 control chromosomes in the GnomAD database, including 276 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 0.024 (120 hom., cov: 32)
  • Exomes 𝑓: 0.017 (156 hom.)
• Consequence: HCP5 ENST00000541196.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• Publications: 3 publications found

Genes affected

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

ENSG00000288587 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0668 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000541196.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	NR_040662.1		n.492T>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	ENST00000541196.3	TSL:1	n.197+254T>C		intron	N/A
	HCP5	ENST00000414046.3	TSL:4	n.502T>C		non_coding_transcript_exon	Exon 2 of 2
	HCP5	ENST00000460889.5	TSL:2	n.406T>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0241 AC: 3664 AN: 151876 Hom.: 120 Cov.: 32

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0246

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.00657

Gnomad SAS AF: 0.0735

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00644

Gnomad OTH AF: 0.0254

GnomAD2 exomes AF: 0.0156 AC: 2614 AN: 167452 AF XY: 0.0162

Gnomad AFR exome AF: 0.0601

Gnomad AMR exome AF: 0.0109

Gnomad ASJ exome AF: 0.0158

Gnomad EAS exome AF: 0.0103

Gnomad FIN exome AF: 0.00191

Gnomad NFE exome AF: 0.00627

Gnomad OTH exome AF: 0.0106

GnomAD4 exome AF: 0.0169 AC: 4780 AN: 282262 Hom.: 156 Cov.: 0 AF XY: 0.0209 AC XY: 3353 AN XY: 160510

African (AFR) AF: 0.0604 AC: 389 AN: 6438

American (AMR) AF: 0.0108 AC: 207 AN: 19224

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 107 AN: 5986

East Asian (EAS) AF: 0.0117 AC: 114 AN: 9738

South Asian (SAS) AF: 0.0559 AC: 2818 AN: 50446

European-Finnish (FIN) AF: 0.00258 AC: 76 AN: 29458

Middle Eastern (MID) AF: 0.0139 AC: 34 AN: 2440

European-Non Finnish (NFE) AF: 0.00581 AC: 849 AN: 146142

Other (OTH) AF: 0.0150 AC: 186 AN: 12390

GnomAD4 genome AF: 0.0241 AC: 3665 AN: 151994 Hom.: 120 Cov.: 32 AF XY: 0.0244 AC XY: 1816 AN XY: 74330

African (AFR) AF: 0.0563 AC: 2329 AN: 41364

American (AMR) AF: 0.0246 AC: 375 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 58 AN: 3470

East Asian (EAS) AF: 0.00678 AC: 35 AN: 5162

South Asian (SAS) AF: 0.0731 AC: 352 AN: 4814

European-Finnish (FIN) AF: 0.00151 AC: 16 AN: 10618

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00643 AC: 437 AN: 68010

Other (OTH) AF: 0.0251 AC: 53 AN: 2112

Alfa AF: 0.0143 Hom.: 82

Bravo AF: 0.0264

Asia WGS AF: 0.0370 AC: 128 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.092
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs17206855; hg19: chr6-31431539; COSMIC: COSV69993903;