rs3099844

Positions:

• chr6-31481199-C-A
• chr6-31481199-C-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.701G>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 0.112 in 151,720 control chromosomes in the GnomAD database, including 1,152 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 0.11 (1152 hom., cov: 32)
• Consequence: MICB-DT NR_149132.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

Genes affected

MICB-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.701G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000656299.1	n.178G>T		non_coding_transcript_exon_variant	2/2
MICB-DT	ENST00000665353.1	n.842G>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16929 AN: 151602 Hom.: 1149 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0612

Gnomad ASJ AF: 0.0645

Gnomad EAS AF: 0.0706

Gnomad SAS AF: 0.0478

Gnomad FIN AF: 0.0811

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0954

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

GnomAD4 genome AF: 0.112 AC: 16942 AN: 151720 Hom.: 1152 Cov.: 32 AF XY: 0.106 AC XY: 7892 AN XY: 74164

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0610

Gnomad4 ASJ AF: 0.0645

Gnomad4 EAS AF: 0.0708

Gnomad4 SAS AF: 0.0480

Gnomad4 FIN AF: 0.0811

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.0944

Alfa AF: 0.111 Hom.: 1904

Bravo AF: 0.113

Asia WGS AF: 0.0640 AC: 223 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3099844; hg19: chr6-31448976;