rs2516424

Positions:

• chr6-31480538-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.1362T>C 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 0.339 in 151,740 control chromosomes in the GnomAD database, including 9,140 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 0.34 (9140 hom., cov: 32)
• Consequence: MICB-DT NR_149132.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505

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 (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.1362T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000665353.1	n.1503T>C		non_coding_transcript_exon_variant	2/2
MICB-DT	ENST00000656299.1	n.839T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51412 AN: 151622 Hom.: 9129 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.339 AC: 51448 AN: 151740 Hom.: 9140 Cov.: 32 AF XY: 0.338 AC XY: 25033 AN XY: 74170

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.325

Alfa AF: 0.336 Hom.: 8181

Bravo AF: 0.343

Asia WGS AF: 0.472 AC: 1640 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	3.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2516424; hg19: chr6-31448315;