chr6-31483699-A-G

Variant names:

• chr6-31483699-A-G
• rs2905747
• ENST00000656299.1:n.68-2390T>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.68-2390T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 151,772 control chromosomes in the GnomAD database, including 53,274 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 0.83 (53274 hom., cov: 31)
• Consequence: MICB-DT ENST00000656299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 25 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.542-2341T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000656299.1	n.68-2390T>C		intron_variant	Intron 1 of 1
MICB-DT	ENST00000665353.2	n.683-2341T>C		intron_variant	Intron 1 of 1
HCP5	ENST00000718213.1	n.96-6963A>G		intron_variant	Intron 1 of 2
HCP5	ENST00000718214.1	n.96-6963A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126433 AN: 151654 Hom.: 53216 Cov.: 31

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.834 AC: 126548 AN: 151772 Hom.: 53274 Cov.: 31 AF XY: 0.832 AC XY: 61716 AN XY: 74176

African (AFR) AF: 0.885 AC: 36523 AN: 41266

American (AMR) AF: 0.882 AC: 13416 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3329 AN: 3468

East Asian (EAS) AF: 0.918 AC: 4738 AN: 5162

South Asian (SAS) AF: 0.924 AC: 4446 AN: 4814

European-Finnish (FIN) AF: 0.669 AC: 7059 AN: 10552

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54216 AN: 67996

Other (OTH) AF: 0.873 AC: 1836 AN: 2104

Alfa AF: 0.821 Hom.: 61664

Bravo AF: 0.853

Asia WGS AF: 0.864 AC: 3005 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.24
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2905747; hg19: chr6-31451476;