chr6-31481492-C-T

Variant names:

• chr6-31481492-C-T
• rs2516422
• ENST00000656299.1:n.68-183G>A

Variant summary

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

The ENST00000656299.1(MICB-DT):​n.68-183G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 151,368 control chromosomes in the GnomAD database, including 3,145 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 0.19 (3145 hom., cov: 30)
• Consequence: MICB-DT ENST00000656299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530
• Publications: 12 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 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.542-134G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	ENST00000656299.1		n.68-183G>A		intron	N/A
	MICB-DT	ENST00000665353.2		n.683-134G>A		intron	N/A
	HCP5	ENST00000718213.1		n.96-9170C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29265 AN: 151252 Hom.: 3142 Cov.: 30

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.193 AC: 29286 AN: 151368 Hom.: 3145 Cov.: 30 AF XY: 0.194 AC XY: 14323 AN XY: 73948

African (AFR) AF: 0.137 AC: 5628 AN: 41112

American (AMR) AF: 0.261 AC: 3953 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 642 AN: 3466

East Asian (EAS) AF: 0.168 AC: 865 AN: 5144

South Asian (SAS) AF: 0.207 AC: 997 AN: 4812

European-Finnish (FIN) AF: 0.162 AC: 1700 AN: 10474

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.217 AC: 14749 AN: 67894

Other (OTH) AF: 0.199 AC: 418 AN: 2100

Alfa AF: 0.198 Hom.: 2532

Bravo AF: 0.201

Asia WGS AF: 0.172 AC: 599 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.3
DANN	Benign	0.84
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2516422; hg19: chr6-31449269;