rs3130914

Variant names:

• chr6-31489609-G-A
• rs3130914
• ENST00000656299.1:n.67+4645C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656299.1(MICB-DT):​n.67+4645C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 149,756 control chromosomes in the GnomAD database, including 6,787 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 0.37 (6787 hom., cov: 35)
• Consequence: MICB-DT ENST00000656299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 5 publications found

Genes affected

MICB-DT (HGNC:53632): (MICB divergent transcript)

HCP5 (HGNC:21659): (HLA complex P5)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656299.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	NR_149132.1		n.541+4645C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	ENST00000656299.1		n.67+4645C>T		intron	N/A
	MICB-DT	ENST00000665353.2		n.682+4645C>T		intron	N/A
	HCP5	ENST00000718213.1		n.96-1053G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 55381 AN: 149640 Hom.: 6770 Cov.: 35

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.390

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.370 AC: 55436 AN: 149756 Hom.: 6787 Cov.: 35 AF XY: 0.372 AC XY: 27207 AN XY: 73182

African (AFR) AF: 0.366 AC: 14951 AN: 40810

American (AMR) AF: 0.351 AC: 5268 AN: 15014

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1130 AN: 3370

East Asian (EAS) AF: 0.478 AC: 2430 AN: 5082

South Asian (SAS) AF: 0.326 AC: 1549 AN: 4754

European-Finnish (FIN) AF: 0.412 AC: 4256 AN: 10332

Middle Eastern (MID) AF: 0.395 AC: 113 AN: 286

European-Non Finnish (NFE) AF: 0.368 AC: 24693 AN: 67142

Other (OTH) AF: 0.348 AC: 726 AN: 2088

Alfa AF: 0.370 Hom.: 731

Asia WGS AF: 0.389 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.37
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs3130914; hg19: chr6-31457386;