rs2534685

Variant names:

• chr6-31494468-C-T
• rs2534685
• ENST00000665353.2:n.468G>A

Variant summary

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

The ENST00000718214.1(HCP5):​n.366C>T variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,780 control chromosomes in the GnomAD database, including 7,710 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 0.31 (7710 hom., cov: 32)
• Consequence: HCP5 ENST00000718214.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 15 publications found

Genes affected

MICB-DT (HGNC:53632): (MICB divergent transcript)

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718214.1. 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
	MICB-DT	NR_149132.1		n.327G>A		non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	ENST00000665353.2		n.468G>A		non_coding_transcript_exon	Exon 1 of 2
	HCP5	ENST00000718214.1		n.366C>T		splice_region non_coding_transcript_exon	Exon 3 of 3
	MICB-DT	ENST00000756008.1		n.147G>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47745 AN: 151662 Hom.: 7701 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.315 AC: 47787 AN: 151780 Hom.: 7710 Cov.: 32 AF XY: 0.310 AC XY: 22989 AN XY: 74168

African (AFR) AF: 0.372 AC: 15370 AN: 41310

American (AMR) AF: 0.213 AC: 3249 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1291 AN: 3464

East Asian (EAS) AF: 0.267 AC: 1376 AN: 5160

South Asian (SAS) AF: 0.298 AC: 1435 AN: 4820

European-Finnish (FIN) AF: 0.282 AC: 2975 AN: 10536

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.311 AC: 21115 AN: 67920

Other (OTH) AF: 0.298 AC: 628 AN: 2110

Alfa AF: 0.325 Hom.: 1174

Bravo AF: 0.314

Asia WGS AF: 0.304 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.84
PhyloP100		0.058
PromoterAI		-0.12	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2534685; hg19: chr6-31462245;