rs3749946

chr6-31481085-C-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.815G>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 0.118 in 151,852 control chromosomes in the GnomAD database, including 1,503 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 0.12 (1503 hom., cov: 32)
• Consequence: MICB-DT NR_149132.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413

Genes affected

MICB-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MICB-DT	NR_149132.1	n.815G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MICB-DT	ENST00000665353.1	n.956G>T		non_coding_transcript_exon_variant	2/2
MICB-DT	ENST00000656299.1	n.292G>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17839 AN: 151734 Hom.: 1498 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0686

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0715

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.118 AC: 17863 AN: 151852 Hom.: 1503 Cov.: 32 AF XY: 0.115 AC XY: 8571 AN XY: 74228

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.0686

Gnomad4 SAS AF: 0.0826

Gnomad4 FIN AF: 0.0670

Gnomad4 NFE AF: 0.0715

Gnomad4 OTH AF: 0.155

Alfa AF: 0.0879 Hom.: 927

Bravo AF: 0.127

Asia WGS AF: 0.100 AC: 345 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.3
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3749946; hg19: chr6-31448862;