chr6-31384263-T-C

Variant names:

• chr6-31384263-T-C
• rs2442749
• ENST00000745027.1:n.568-1073A>G

Variant summary

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

The ENST00000745027.1(MICA-AS1):​n.568-1073A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,858 control chromosomes in the GnomAD database, including 4,644 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 0.23 (4644 hom., cov: 31)
• Consequence: MICA-AS1 ENST00000745027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 23 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICA-AS1	ENST00000745027.1		n.568-1073A>G		intron	N/A
	MICA-AS1	ENST00000745028.1		n.331-1073A>G		intron	N/A
	MICA-AS1	ENST00000745029.1		n.232+649A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35664 AN: 151740 Hom.: 4646 Cov.: 31

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.235 AC: 35674 AN: 151858 Hom.: 4644 Cov.: 31 AF XY: 0.230 AC XY: 17090 AN XY: 74222

African (AFR) AF: 0.142 AC: 5864 AN: 41432

American (AMR) AF: 0.225 AC: 3436 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1382 AN: 3460

East Asian (EAS) AF: 0.217 AC: 1122 AN: 5166

South Asian (SAS) AF: 0.160 AC: 772 AN: 4814

European-Finnish (FIN) AF: 0.271 AC: 2860 AN: 10558

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.286 AC: 19415 AN: 67868

Other (OTH) AF: 0.218 AC: 458 AN: 2104

Alfa AF: 0.276 Hom.: 19219

Bravo AF: 0.230

Asia WGS AF: 0.187 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.5
DANN	Benign	0.77
PhyloP100		0.19

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2442749;

hg19: chr6-31352040;