6-31494544-G-T

Variant names:

• chr6-31494544-G-T
• rs2516412
• ENST00000665353.2:n.392C>A

Variant summary

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

The ENST00000665353.2(MICB-DT):​n.392C>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 0.315 in 152,044 control chromosomes in the GnomAD database, including 7,793 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 0.32 (7793 hom., cov: 33)
• Consequence: MICB-DT ENST00000665353.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.251C>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000665353.2	n.392C>A		non_coding_transcript_exon_variant	Exon 1 of 2
MICB-DT	ENST00000756008.1	n.71C>A		non_coding_transcript_exon_variant	Exon 1 of 2
MICB-DT	ENST00000656299.1	n.-224C>A		upstream_gene_variant
HCP5	ENST00000718214.1	n.*74G>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47920 AN: 151928 Hom.: 7784 Cov.: 33

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.375

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.315 AC: 47962 AN: 152044 Hom.: 7793 Cov.: 33 AF XY: 0.311 AC XY: 23084 AN XY: 74316

African (AFR) AF: 0.373 AC: 15462 AN: 41444

American (AMR) AF: 0.213 AC: 3252 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1295 AN: 3472

East Asian (EAS) AF: 0.269 AC: 1385 AN: 5158

South Asian (SAS) AF: 0.299 AC: 1443 AN: 4832

European-Finnish (FIN) AF: 0.283 AC: 2991 AN: 10554

Middle Eastern (MID) AF: 0.386 AC: 112 AN: 290

European-Non Finnish (NFE) AF: 0.311 AC: 21154 AN: 67972

Other (OTH) AF: 0.298 AC: 631 AN: 2116

Alfa AF: 0.353 Hom.: 7242

Bravo AF: 0.314

Asia WGS AF: 0.305 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
DANN	Benign	0.78
PhyloP100		-0.22
PromoterAI		0.061	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2516412; hg19: chr6-31462321;