rs2523647

Positions:

• chr6-31482001-A-G

Variant summary

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

The NR_149132.1(MICB-DT):​n.542-643T>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 NR_149132.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

Genes affected

MICB-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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/exons	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.542-643T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000656299.1	n.68-692T>C		intron_variant
MICB-DT	ENST00000665353.1	n.683-643T>C		intron_variant

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

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.231

Alfa AF: 0.229 Hom.: 3331

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523647; hg19: chr6-31449778;