ENST00000745027.1:n.733C>T

Variant names:

• chr6-31383025-G-A
• rs2844533
• ENST00000745027.1:n.733C>T

Variant summary

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

The ENST00000745027.1(MICA-AS1):​n.733C>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 0.749 in 152,028 control chromosomes in the GnomAD database, including 43,055 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 0.75 (43055 hom., cov: 31)
• Consequence: MICA-AS1 ENST00000745027.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 35 publications found

Genes affected

MICA-AS1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745027.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICA-AS1	ENST00000745027.1		n.733C>T		non_coding_transcript_exon	Exon 2 of 2
	MICA-AS1	ENST00000745028.1		n.496C>T		non_coding_transcript_exon	Exon 2 of 2
	MICA-AS1	ENST00000745029.1		n.398C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113779 AN: 151910 Hom.: 43011 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.749 AC: 113873 AN: 152028 Hom.: 43055 Cov.: 31 AF XY: 0.756 AC XY: 56216 AN XY: 74322

African (AFR) AF: 0.677 AC: 28027 AN: 41426

American (AMR) AF: 0.767 AC: 11719 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2977 AN: 3470

East Asian (EAS) AF: 0.925 AC: 4787 AN: 5174

South Asian (SAS) AF: 0.839 AC: 4039 AN: 4816

European-Finnish (FIN) AF: 0.832 AC: 8791 AN: 10570

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50917 AN: 67978

Other (OTH) AF: 0.740 AC: 1564 AN: 2114

Alfa AF: 0.755 Hom.: 172188

Bravo AF: 0.735

Asia WGS AF: 0.866 AC: 3013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.5
DANN	Benign	0.88
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2844533; hg19: chr6-31350802; COSMIC: COSV69645936;