6-31493312-A-G

Position:

• chr6-31493312-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.541+942T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,096 control chromosomes in the GnomAD database, including 31,917 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 0.65 (31917 hom., cov: 32)
• Consequence: MICB-DT NR_149132.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58

Genes affected

MICB-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.541+942T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000656299.1	n.67+942T>C		intron_variant
MICB-DT	ENST00000665353.1	n.682+942T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98042 AN: 151978 Hom.: 31867 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.645 AC: 98138 AN: 152096 Hom.: 31917 Cov.: 32 AF XY: 0.647 AC XY: 48113 AN XY: 74366

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.614

Alfa AF: 0.665 Hom.: 62589

Bravo AF: 0.647

Asia WGS AF: 0.624 AC: 2176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130922; hg19: chr6-31461089;