chr6-31484059-T-C

Variant names:

• chr6-31484059-T-C
• rs3094011
• ENST00000656299.1:n.68-2750A>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.542-2701A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 151,894 control chromosomes in the GnomAD database, including 1,146 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 0.11 (1146 hom., cov: 32)
• Consequence: MICB-DT NR_149132.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 27 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 (AFR) allele frequency at 95% confidence interval = 0.136 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.542-2701A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	ENST00000656299.1		n.68-2750A>G		intron	N/A
	MICB-DT	ENST00000665353.2		n.683-2701A>G		intron	N/A
	HCP5	ENST00000718213.1		n.96-6603T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16901 AN: 151776 Hom.: 1143 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.0639

Gnomad EAS AF: 0.0713

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.111 AC: 16914 AN: 151894 Hom.: 1146 Cov.: 32 AF XY: 0.106 AC XY: 7873 AN XY: 74264

African (AFR) AF: 0.139 AC: 5726 AN: 41324

American (AMR) AF: 0.0615 AC: 936 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0639 AC: 221 AN: 3460

East Asian (EAS) AF: 0.0715 AC: 369 AN: 5164

South Asian (SAS) AF: 0.0476 AC: 230 AN: 4828

European-Finnish (FIN) AF: 0.0812 AC: 860 AN: 10594

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8214 AN: 67984

Other (OTH) AF: 0.0947 AC: 200 AN: 2112

Alfa AF: 0.123 Hom.: 2354

Bravo AF: 0.113

Asia WGS AF: 0.0640 AC: 223 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.43
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3094011; hg19: chr6-31451836;