chr6-31481199-C-A

Variant names:

• chr6-31481199-C-A
• rs3099844
• ENST00000656299.1:n.178G>T

Variant summary

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

The ENST00000656299.1(MICB-DT):​n.178G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 151,720 control chromosomes in the GnomAD database, including 1,152 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 (1152 hom., cov: 32)
• Consequence: MICB-DT ENST00000656299.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 111 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=-0.91).
• 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: 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.701G>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	ENST00000656299.1		n.178G>T		non_coding_transcript_exon	Exon 2 of 2
	MICB-DT	ENST00000665353.2		n.842G>T		non_coding_transcript_exon	Exon 2 of 2
	HCP5	ENST00000718213.1		n.96-9463C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16929 AN: 151602 Hom.: 1149 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0612

Gnomad ASJ AF: 0.0645

Gnomad EAS AF: 0.0706

Gnomad SAS AF: 0.0478

Gnomad FIN AF: 0.0811

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0954

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

GnomAD4 genome AF: 0.112 AC: 16942 AN: 151720 Hom.: 1152 Cov.: 32 AF XY: 0.106 AC XY: 7892 AN XY: 74164

African (AFR) AF: 0.139 AC: 5755 AN: 41264

American (AMR) AF: 0.0610 AC: 927 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.0645 AC: 223 AN: 3456

East Asian (EAS) AF: 0.0708 AC: 366 AN: 5172

South Asian (SAS) AF: 0.0480 AC: 231 AN: 4808

European-Finnish (FIN) AF: 0.0811 AC: 857 AN: 10568

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.121 AC: 8226 AN: 67954

Other (OTH) AF: 0.0944 AC: 199 AN: 2108

Alfa AF: 0.119 Hom.: 4097

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	-0.91
CADD	Benign	2.0
DANN	Benign	0.39
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs3099844; hg19: chr6-31448976;