rs2507971

Positions:

• chr6-31493595-A-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+659T>A 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 0.595 in 151,948 control chromosomes in the GnomAD database, including 27,273 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 0.60 (27273 hom., cov: 32)
• Consequence: MICB-DT NR_149132.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

Genes affected

MICB-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.541+659T>A		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+659T>A		intron_variant, non_coding_transcript_variant
MICB-DT	ENST00000656299.1	n.67+659T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90393 AN: 151828 Hom.: 27252 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.595 AC: 90453 AN: 151948 Hom.: 27273 Cov.: 32 AF XY: 0.594 AC XY: 44095 AN XY: 74264

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.573

Alfa AF: 0.599 Hom.: 3440

Bravo AF: 0.608

Asia WGS AF: 0.616 AC: 2146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2507971; hg19: chr6-31461372;