6-31493836-T-C

Variant names:

• chr6-31493836-T-C
• rs2252937
• ENST00000656299.1:n.67+418A>G

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+418A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,166 control chromosomes in the GnomAD database, including 2,489 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 0.18 (2489 hom., cov: 34)
• Consequence: MICB-DT NR_149132.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 4 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	NR_149132.1		n.541+418A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	ENST00000656299.1		n.67+418A>G		intron	N/A
	MICB-DT	ENST00000665353.2		n.682+418A>G		intron	N/A
	HCP5	ENST00000718214.1		n.156-422T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26486 AN: 151062 Hom.: 2493 Cov.: 34

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0452

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.175 AC: 26479 AN: 151166 Hom.: 2489 Cov.: 34 AF XY: 0.175 AC XY: 12934 AN XY: 73914

African (AFR) AF: 0.196 AC: 8000 AN: 40910

American (AMR) AF: 0.192 AC: 2913 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 706 AN: 3438

East Asian (EAS) AF: 0.0453 AC: 232 AN: 5116

South Asian (SAS) AF: 0.0871 AC: 415 AN: 4766

European-Finnish (FIN) AF: 0.209 AC: 2213 AN: 10588

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.167 AC: 11304 AN: 67850

Other (OTH) AF: 0.223 AC: 468 AN: 2096

Alfa AF: 0.0698 Hom.: 72

Bravo AF: 0.181

Asia WGS AF: 0.0700 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	7.5
DANN	Benign	0.38
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs2252937; hg19: chr6-31461613;