rs2263318

Variant names:

• chr6-31464229-G-A
• rs2263318
• ENST00000541196.3:n.276-56G>A

Variant summary

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

The ENST00000414046.3(HCP5):​n.969G>A 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 0.0858 in 185,098 control chromosomes in the GnomAD database, including 1,018 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 0.095 (964 hom., cov: 32)
  • Exomes 𝑓: 0.042 (54 hom.)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 10 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414046.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	NR_040662.1		n.959G>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	ENST00000541196.3	TSL:1	n.276-56G>A		intron	N/A
	HCP5	ENST00000414046.3	TSL:4	n.969G>A		non_coding_transcript_exon	Exon 2 of 2
	HCP5	ENST00000670109.1		n.932G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0954 AC: 14497 AN: 151894 Hom.: 964 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0773

Gnomad OTH AF: 0.121

GnomAD4 exome AF: 0.0422 AC: 1396 AN: 33086 Hom.: 54 Cov.: 0 AF XY: 0.0390 AC XY: 742 AN XY: 19034

African (AFR) AF: 0.142 AC: 103 AN: 724

American (AMR) AF: 0.0971 AC: 88 AN: 906

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 70 AN: 538

East Asian (EAS) AF: 0.0286 AC: 44 AN: 1536

South Asian (SAS) AF: 0.0114 AC: 73 AN: 6378

European-Finnish (FIN) AF: 0.0138 AC: 71 AN: 5156

Middle Eastern (MID) AF: 0.0806 AC: 10 AN: 124

European-Non Finnish (NFE) AF: 0.0542 AC: 880 AN: 16244

Other (OTH) AF: 0.0385 AC: 57 AN: 1480

GnomAD4 genome AF: 0.0953 AC: 14494 AN: 152012 Hom.: 964 Cov.: 32 AF XY: 0.0905 AC XY: 6730 AN XY: 74338

African (AFR) AF: 0.149 AC: 6166 AN: 41364

American (AMR) AF: 0.126 AC: 1923 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3468

East Asian (EAS) AF: 0.0164 AC: 85 AN: 5174

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4820

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10626

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0773 AC: 5254 AN: 67994

Other (OTH) AF: 0.119 AC: 251 AN: 2112

Alfa AF: 0.0901 Hom.: 124

Bravo AF: 0.110

Asia WGS AF: 0.0290 AC: 101 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.6
DANN	Benign	0.79
PhyloP100		0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2263318;

hg19: chr6-31432006;