6-31493312-A-G

Variant names:

• chr6-31493312-A-G
• rs3130922
• ENST00000656299.1:n.67+942T>C

Variant summary

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

The NR_149132.1(MICB-DT):​n.541+942T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,096 control chromosomes in the GnomAD database, including 31,917 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 0.65 (31917 hom., cov: 32)
• Consequence: MICB-DT NR_149132.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58
• Publications: 39 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_149132.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	NR_149132.1		n.541+942T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	ENST00000656299.1		n.67+942T>C		intron	N/A
	MICB-DT	ENST00000665353.2		n.682+942T>C		intron	N/A
	HCP5	ENST00000718214.1		n.156-946A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98042 AN: 151978 Hom.: 31867 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.645 AC: 98138 AN: 152096 Hom.: 31917 Cov.: 32 AF XY: 0.647 AC XY: 48113 AN XY: 74366

African (AFR) AF: 0.586 AC: 24298 AN: 41436

American (AMR) AF: 0.678 AC: 10365 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2177 AN: 3472

East Asian (EAS) AF: 0.737 AC: 3822 AN: 5188

South Asian (SAS) AF: 0.587 AC: 2832 AN: 4826

European-Finnish (FIN) AF: 0.679 AC: 7179 AN: 10566

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45244 AN: 68002

Other (OTH) AF: 0.614 AC: 1300 AN: 2116

Alfa AF: 0.663 Hom.: 138416

Bravo AF: 0.647

Asia WGS AF: 0.624 AC: 2176 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	1.2
DANN	Benign	0.44
PhyloP100		-3.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3130922;

hg19: chr6-31461089;