6-31383665-A-T

Variant names:

• chr6-31383665-A-T
• rs3099848
• ENST00000745027.1:n.568-475T>A

Variant summary

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

The ENST00000745027.1(MICA-AS1):​n.568-475T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,178 control chromosomes in the GnomAD database, including 38,265 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 0.71 (38265 hom., cov: 32)
• Consequence: MICA-AS1 ENST00000745027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 4 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 = 0.76 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.568-475T>A		intron	N/A
	MICA-AS1	ENST00000745028.1		n.331-475T>A		intron	N/A
	MICA-AS1	ENST00000745029.1		n.233-475T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107486 AN: 152060 Hom.: 38227 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.707 AC: 107577 AN: 152178 Hom.: 38265 Cov.: 32 AF XY: 0.705 AC XY: 52468 AN XY: 74388

African (AFR) AF: 0.645 AC: 26761 AN: 41500

American (AMR) AF: 0.772 AC: 11804 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2789 AN: 3470

East Asian (EAS) AF: 0.573 AC: 2964 AN: 5176

South Asian (SAS) AF: 0.755 AC: 3638 AN: 4820

European-Finnish (FIN) AF: 0.707 AC: 7489 AN: 10586

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49521 AN: 68016

Other (OTH) AF: 0.735 AC: 1553 AN: 2114

Alfa AF: 0.707 Hom.: 4504

Bravo AF: 0.708

Asia WGS AF: 0.677 AC: 2356 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	7.4
DANN	Benign	0.22
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs3099848; hg19: chr6-31351442;