rs3749946

Variant names:

• chr6-31481085-C-A
• rs3749946
• ENST00000656299.1:n.292G>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.292G>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 0.118 in 151,852 control chromosomes in the GnomAD database, including 1,503 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 0.12 (1503 hom., cov: 32)
• Consequence: MICB-DT ENST00000656299.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413
• 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 (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.815G>T		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.292G>T		non_coding_transcript_exon_variant	Exon 2 of 2
MICB-DT	ENST00000665353.2	n.956G>T		non_coding_transcript_exon_variant	Exon 2 of 2
HCP5	ENST00000718213.1	n.96-9577C>A		intron_variant	Intron 1 of 2
HCP5	ENST00000718214.1	n.96-9577C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17839 AN: 151734 Hom.: 1498 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0686

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0715

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.118 AC: 17863 AN: 151852 Hom.: 1503 Cov.: 32 AF XY: 0.115 AC XY: 8571 AN XY: 74228

African (AFR) AF: 0.205 AC: 8453 AN: 41292

American (AMR) AF: 0.116 AC: 1760 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 916 AN: 3462

East Asian (EAS) AF: 0.0686 AC: 355 AN: 5174

South Asian (SAS) AF: 0.0826 AC: 398 AN: 4816

European-Finnish (FIN) AF: 0.0670 AC: 709 AN: 10582

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0715 AC: 4862 AN: 68000

Other (OTH) AF: 0.155 AC: 327 AN: 2112

Alfa AF: 0.0917 Hom.: 2966

Bravo AF: 0.127

Asia WGS AF: 0.100 AC: 345 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	3.3
DANN	Benign	0.49
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs3749946; hg19: chr6-31448862;