6-31483699-A-G

Position:

• chr6-31483699-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.542-2341T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 151,772 control chromosomes in the GnomAD database, including 53,274 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 0.83 (53274 hom., cov: 31)
• Consequence: MICB-DT NR_149132.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84

Genes affected

MICB-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MICB-DT	NR_149132.1	n.542-2341T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MICB-DT	ENST00000665353.1	n.683-2341T>C		intron_variant, non_coding_transcript_variant
MICB-DT	ENST00000656299.1	n.68-2390T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126433 AN: 151654 Hom.: 53216 Cov.: 31

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.834 AC: 126548 AN: 151772 Hom.: 53274 Cov.: 31 AF XY: 0.832 AC XY: 61716 AN XY: 74176

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.960

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.873

Alfa AF: 0.817 Hom.: 41101

Bravo AF: 0.853

Asia WGS AF: 0.864 AC: 3005 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2905747; hg19: chr6-31451476;