6-31491965-G-A

Variant names:

• chr6-31491965-G-A
• rs2516415
• ENST00000656299.1:n.67+2289C>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.67+2289C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,118 control chromosomes in the GnomAD database, including 8,088 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 0.32 (8088 hom., cov: 33)
• Consequence: MICB-DT ENST00000656299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 38 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.541+2289C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000656299.1	n.67+2289C>T		intron_variant	Intron 1 of 1
MICB-DT	ENST00000665353.2	n.682+2289C>T		intron_variant	Intron 1 of 1
HCP5	ENST00000718213.1	n.156-140G>A		intron_variant	Intron 2 of 2
HCP5	ENST00000718214.1	n.155+1244G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48961 AN: 152000 Hom.: 8075 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.322 AC: 48996 AN: 152118 Hom.: 8088 Cov.: 33 AF XY: 0.321 AC XY: 23849 AN XY: 74362

African (AFR) AF: 0.298 AC: 12368 AN: 41474

American (AMR) AF: 0.322 AC: 4922 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1271 AN: 3466

East Asian (EAS) AF: 0.533 AC: 2757 AN: 5174

South Asian (SAS) AF: 0.294 AC: 1419 AN: 4824

European-Finnish (FIN) AF: 0.297 AC: 3137 AN: 10574

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22148 AN: 67998

Other (OTH) AF: 0.295 AC: 623 AN: 2112

Alfa AF: 0.339 Hom.: 26973

Bravo AF: 0.326

Asia WGS AF: 0.379 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.5
DANN	Benign	0.76
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs2516415; hg19: chr6-31459742;