chr6-31492366-T-C

Variant names:

• chr6-31492366-T-C
• rs2395034
• ENST00000656299.1:n.67+1888A>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+1888A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,136 control chromosomes in the GnomAD database, including 3,360 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 0.20 (3360 hom., cov: 32)
• Consequence: MICB-DT NR_149132.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730
• Publications: 10 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.268 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+1888A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	ENST00000656299.1		n.67+1888A>G		intron	N/A
	MICB-DT	ENST00000665353.2		n.682+1888A>G		intron	N/A
	HCP5	ENST00000718214.1		n.155+1645T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31015 AN: 152016 Hom.: 3358 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.204 AC: 31036 AN: 152136 Hom.: 3360 Cov.: 32 AF XY: 0.204 AC XY: 15182 AN XY: 74362

African (AFR) AF: 0.155 AC: 6420 AN: 41512

American (AMR) AF: 0.275 AC: 4200 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 702 AN: 3466

East Asian (EAS) AF: 0.183 AC: 949 AN: 5186

South Asian (SAS) AF: 0.228 AC: 1100 AN: 4816

European-Finnish (FIN) AF: 0.162 AC: 1718 AN: 10586

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15144 AN: 67982

Other (OTH) AF: 0.213 AC: 449 AN: 2110

Alfa AF: 0.209 Hom.: 524

Bravo AF: 0.212

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.3
DANN	Benign	0.33
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs2395034; hg19: chr6-31460143;