rs3130923

chr6-31494358-G-Achr6-31494358-G-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.437C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0985 in 152,178 control chromosomes in the GnomAD database, including 825 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 0.098 (825 hom., cov: 33)
• Consequence: MICB-DT NR_149132.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

MICB-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MICB-DT	NR_149132.1	n.437C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MICB-DT	ENST00000665353.1	n.578C>T		non_coding_transcript_exon_variant	1/2
MICB-DT	ENST00000656299.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0985 AC: 14978 AN: 152060 Hom.: 824 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0473

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0811

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0985 AC: 14986 AN: 152178 Hom.: 825 Cov.: 33 AF XY: 0.0934 AC XY: 6952 AN XY: 74402

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0471

Gnomad4 ASJ AF: 0.0429

Gnomad4 EAS AF: 0.0619

Gnomad4 SAS AF: 0.0375

Gnomad4 FIN AF: 0.0811

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.0498 Hom.: 63

Bravo AF: 0.0978

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.9
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130923; hg19: chr6-31462135;