rs2523647

Variant names:

• chr6-31482001-A-G
• rs2523647
• ENST00000656299.1:n.68-692T>C

Variant summary

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

The ENST00000656299.1(MICB-DT):​n.68-692T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,710 control chromosomes in the GnomAD database, including 4,508 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 0.23 (4508 hom., cov: 31)
• Consequence: MICB-DT ENST00000656299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 26 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.542-643T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000656299.1	n.68-692T>C		intron_variant	Intron 1 of 1
MICB-DT	ENST00000665353.2	n.683-643T>C		intron_variant	Intron 1 of 1
HCP5	ENST00000718213.1	n.96-8661A>G		intron_variant	Intron 1 of 2
HCP5	ENST00000718214.1	n.96-8661A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34529 AN: 151592 Hom.: 4503 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.228 AC: 34552 AN: 151710 Hom.: 4508 Cov.: 31 AF XY: 0.232 AC XY: 17177 AN XY: 74134

African (AFR) AF: 0.164 AC: 6766 AN: 41246

American (AMR) AF: 0.288 AC: 4387 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1125 AN: 3468

East Asian (EAS) AF: 0.519 AC: 2670 AN: 5140

South Asian (SAS) AF: 0.310 AC: 1489 AN: 4800

European-Finnish (FIN) AF: 0.227 AC: 2398 AN: 10556

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14974 AN: 67968

Other (OTH) AF: 0.231 AC: 486 AN: 2106

Alfa AF: 0.232 Hom.: 7727

Bravo AF: 0.230

Asia WGS AF: 0.408 AC: 1418 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.69
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2523647; hg19: chr6-31449778;