rs3130914

Positions:

• chr6-31489609-G-A

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+4645C>T 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 0.37 in 149,756 control chromosomes in the GnomAD database, including 6,787 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 0.37 (6787 hom., cov: 35)
• Consequence: MICB-DT NR_149132.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

MICB-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MICB-DT	NR_149132.1	n.541+4645C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MICB-DT	ENST00000665353.1	n.682+4645C>T		intron_variant, non_coding_transcript_variant
MICB-DT	ENST00000656299.1	n.67+4645C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.370 AC: 55381 AN: 149640 Hom.: 6770 Cov.: 35

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.390

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.370 AC: 55436 AN: 149756 Hom.: 6787 Cov.: 35 AF XY: 0.372 AC XY: 27207 AN XY: 73182

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.348

Alfa AF: 0.370 Hom.: 731

Asia WGS AF: 0.389 AC: 1355 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	0.47
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130914; hg19: chr6-31457386;