rs2516415

Positions:

• chr6-31491965-G-A
• chr6-31491965-G-C
• chr6-31491965-G-T

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+2289C>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 0.322 in 152,118 control chromosomes in the GnomAD database, including 8,088 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 0.32 (8088 hom., cov: 33)
• Consequence: MICB-DT NR_149132.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

Genes affected

MICB-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.541+2289C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000665353.1	n.682+2289C>T		intron_variant, non_coding_transcript_variant
MICB-DT	ENST00000656299.1	n.67+2289C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48961 AN: 152000 Hom.: 8075 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.322 AC: 48996 AN: 152118 Hom.: 8088 Cov.: 33 AF XY: 0.321 AC XY: 23849 AN XY: 74362

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.295

Alfa AF: 0.331 Hom.: 8911

Bravo AF: 0.326

Asia WGS AF: 0.379 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2516415; hg19: chr6-31459742;