ENST00000665353.1:n.392C>A

Variant names:

• chr6-31494544-G-T
• rs2516412
• ENST00000665353.1:n.392C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665353.1(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 ENST00000665353.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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	ENST00000665353.1	n.392C>A		non_coding_transcript_exon_variant	Exon 1 of 2
MICB-DT	ENST00000656299.1	n.-224C>A		upstream_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

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.298

Alfa AF: 0.327 Hom.: 1480

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2516412; hg19: chr6-31462321;