rs2516424

Variant names:

• chr6-31480538-A-G
• rs2516424
• ENST00000656299.1:n.839T>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.839T>C 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 0.339 in 151,740 control chromosomes in the GnomAD database, including 9,140 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 0.34 (9140 hom., cov: 32)
• Consequence: MICB-DT ENST00000656299.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505
• Publications: 31 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.1362T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000656299.1	n.839T>C		non_coding_transcript_exon_variant	Exon 2 of 2
MICB-DT	ENST00000665353.2	n.1503T>C		non_coding_transcript_exon_variant	Exon 2 of 2
HCP5	ENST00000718213.1	n.96-10124A>G		intron_variant	Intron 1 of 2
HCP5	ENST00000718214.1	n.96-10124A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51412 AN: 151622 Hom.: 9129 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.339 AC: 51448 AN: 151740 Hom.: 9140 Cov.: 32 AF XY: 0.338 AC XY: 25033 AN XY: 74170

African (AFR) AF: 0.302 AC: 12479 AN: 41298

American (AMR) AF: 0.349 AC: 5311 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1351 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3038 AN: 5138

South Asian (SAS) AF: 0.357 AC: 1715 AN: 4804

European-Finnish (FIN) AF: 0.308 AC: 3254 AN: 10562

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.341 AC: 23202 AN: 67954

Other (OTH) AF: 0.325 AC: 685 AN: 2110

Alfa AF: 0.340 Hom.: 12214

Bravo AF: 0.343

Asia WGS AF: 0.472 AC: 1640 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.43
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs2516424; hg19: chr6-31448315;