6-31384336-T-C

Variant names:

• chr6-31384336-T-C
• rs9266772
• ENST00000745027.1:n.568-1146A>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.568-1146A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 151,756 control chromosomes in the GnomAD database, including 2,850 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 0.18 (2850 hom., cov: 30)
• Consequence: MICA-AS1 ENST00000745027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.244 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.568-1146A>G		intron	N/A
	MICA-AS1	ENST00000745028.1		n.331-1146A>G		intron	N/A
	MICA-AS1	ENST00000745029.1		n.232+576A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27688 AN: 151638 Hom.: 2847 Cov.: 30

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0889

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.183 AC: 27715 AN: 151756 Hom.: 2850 Cov.: 30 AF XY: 0.179 AC XY: 13243 AN XY: 74180

African (AFR) AF: 0.180 AC: 7448 AN: 41348

American (AMR) AF: 0.251 AC: 3828 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3466

East Asian (EAS) AF: 0.0895 AC: 461 AN: 5152

South Asian (SAS) AF: 0.206 AC: 990 AN: 4800

European-Finnish (FIN) AF: 0.0998 AC: 1055 AN: 10574

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12864 AN: 67862

Other (OTH) AF: 0.215 AC: 453 AN: 2104

Alfa AF: 0.184 Hom.: 7032

Bravo AF: 0.196

Asia WGS AF: 0.185 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.3
DANN	Benign	0.58
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs9266772; hg19: chr6-31352113;