rs2534685

Positions:

• chr6-31494468-C-T

Variant summary

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

The NR_149132.1(MICB-DT):​n.327G>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 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: MICB-DT NR_149132.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

Genes affected

MICB-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.327G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000665353.1	n.468G>A		non_coding_transcript_exon_variant	1/2

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

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.298

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2534685; hg19: chr6-31462245;