6-31493836-T-C

Position:

• chr6-31493836-T-C

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+418A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,166 control chromosomes in the GnomAD database, including 2,489 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 0.18 (2489 hom., cov: 34)
• Consequence: MICB-DT NR_149132.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

Genes affected

MICB-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.541+418A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000656299.1	n.67+418A>G		intron_variant
MICB-DT	ENST00000665353.1	n.682+418A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26486 AN: 151062 Hom.: 2493 Cov.: 34

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0452

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.175 AC: 26479 AN: 151166 Hom.: 2489 Cov.: 34 AF XY: 0.175 AC XY: 12934 AN XY: 73914

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0453

Gnomad4 SAS AF: 0.0871

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.223

Alfa AF: 0.0698 Hom.: 72

Bravo AF: 0.181

Asia WGS AF: 0.0700 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	7.5
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2252937; hg19: chr6-31461613;