ENST00000656299.1:n.68-241T>C

Variant names:

• chr6-31481550-A-G
• rs2905722
• ENST00000656299.1:n.68-241T>C

Variant summary

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

The ENST00000656299.1(MICB-DT):​n.68-241T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 151,790 control chromosomes in the GnomAD database, including 59,666 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 0.89 (59666 hom., cov: 31)
• Consequence: MICB-DT ENST00000656299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 26 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	NR_149132.1		n.542-192T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	ENST00000656299.1		n.68-241T>C		intron	N/A
	MICB-DT	ENST00000665353.2		n.683-192T>C		intron	N/A
	HCP5	ENST00000718213.1		n.96-9112A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.885 AC: 134263 AN: 151672 Hom.: 59608 Cov.: 31

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.955

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.885 AC: 134380 AN: 151790 Hom.: 59666 Cov.: 31 AF XY: 0.887 AC XY: 65824 AN XY: 74184

African (AFR) AF: 0.897 AC: 37005 AN: 41250

American (AMR) AF: 0.914 AC: 13899 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3381 AN: 3470

East Asian (EAS) AF: 0.977 AC: 5053 AN: 5174

South Asian (SAS) AF: 0.900 AC: 4327 AN: 4810

European-Finnish (FIN) AF: 0.875 AC: 9252 AN: 10574

Middle Eastern (MID) AF: 0.949 AC: 277 AN: 292

European-Non Finnish (NFE) AF: 0.858 AC: 58364 AN: 68002

Other (OTH) AF: 0.918 AC: 1934 AN: 2106

Alfa AF: 0.872 Hom.: 194018

Bravo AF: 0.891

Asia WGS AF: 0.935 AC: 3250 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.9
DANN	Benign	0.63
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2905722; hg19: chr6-31449327;