chr6-31480756-C-T

Variant names:

• chr6-31480756-C-T
• rs2248617
• ENST00000656299.1:n.621G>A

Variant summary

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

The ENST00000656299.1(MICB-DT):​n.621G>A 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 151,670 control chromosomes in the GnomAD database, including 9,157 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 (9157 hom., cov: 32)
• Consequence: MICB-DT ENST00000656299.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407
• Publications: 37 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=-0.96).
• 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.1144G>A		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.621G>A		non_coding_transcript_exon_variant	Exon 2 of 2
MICB-DT	ENST00000665353.2	n.1285G>A		non_coding_transcript_exon_variant	Exon 2 of 2
HCP5	ENST00000718213.1	n.96-9906C>T		intron_variant	Intron 1 of 2
HCP5	ENST00000718214.1	n.96-9906C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51452 AN: 151552 Hom.: 9146 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.339 AC: 51488 AN: 151670 Hom.: 9157 Cov.: 32 AF XY: 0.338 AC XY: 25052 AN XY: 74092

African (AFR) AF: 0.303 AC: 12495 AN: 41242

American (AMR) AF: 0.349 AC: 5301 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3468

East Asian (EAS) AF: 0.591 AC: 3043 AN: 5148

South Asian (SAS) AF: 0.359 AC: 1720 AN: 4796

European-Finnish (FIN) AF: 0.310 AC: 3265 AN: 10548

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

European-Non Finnish (NFE) AF: 0.342 AC: 23216 AN: 67970

Other (OTH) AF: 0.324 AC: 682 AN: 2106

Alfa AF: 0.356 Hom.: 30128

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	-0.96
CADD	Benign	4.6
DANN	Benign	0.81
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2248617; hg19: chr6-31448533;