rs3130923

Variant names:

• chr6-31494358-G-A
• rs3130923
• ENST00000665353.2:n.578C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-31494358-G-A
• chr6-31494358-G-C

Variant summary

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

The ENST00000665353.2(MICB-DT):​n.578C>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 0.0985 in 152,178 control chromosomes in the GnomAD database, including 825 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 0.098 (825 hom., cov: 33)
• Consequence: MICB-DT ENST00000665353.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 18 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICB-DT	NR_149132.1	n.437C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICB-DT	ENST00000665353.2	n.578C>T		non_coding_transcript_exon_variant	Exon 1 of 2
HCP5	ENST00000718214.1	n.256G>A		non_coding_transcript_exon_variant	Exon 3 of 3
MICB-DT	ENST00000756008.1	n.257C>T		non_coding_transcript_exon_variant	Exon 1 of 2
MICB-DT	ENST00000656299.1	n.-38C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0985 AC: 14978 AN: 152060 Hom.: 824 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0473

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0811

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0985 AC: 14986 AN: 152178 Hom.: 825 Cov.: 33 AF XY: 0.0934 AC XY: 6952 AN XY: 74402

African (AFR) AF: 0.110 AC: 4562 AN: 41500

American (AMR) AF: 0.0471 AC: 721 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3472

East Asian (EAS) AF: 0.0619 AC: 320 AN: 5170

South Asian (SAS) AF: 0.0375 AC: 181 AN: 4826

European-Finnish (FIN) AF: 0.0811 AC: 860 AN: 10604

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7892 AN: 67986

Other (OTH) AF: 0.0724 AC: 153 AN: 2114

Alfa AF: 0.0522 Hom.: 66

Bravo AF: 0.0978

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.87
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs3130923; hg19: chr6-31462135;