rs7775759

Variant names:

• chr6-31384669-G-A
• rs7775759
• ENST00000745027.1:n.568-1479C>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.568-1479C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,102 control chromosomes in the GnomAD database, including 10,252 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 0.36 (10252 hom., cov: 32)
• Consequence: MICA-AS1 ENST00000745027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 11 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 (AMR) allele frequency at 95% confidence interval = 0.416 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICA-AS1	ENST00000745027.1		n.568-1479C>T		intron	N/A
	MICA-AS1	ENST00000745028.1		n.331-1479C>T		intron	N/A
	MICA-AS1	ENST00000745029.1		n.232+243C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54805 AN: 151984 Hom.: 10239 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.361 AC: 54861 AN: 152102 Hom.: 10252 Cov.: 32 AF XY: 0.366 AC XY: 27245 AN XY: 74346

African (AFR) AF: 0.381 AC: 15804 AN: 41484

American (AMR) AF: 0.424 AC: 6489 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2094 AN: 3468

East Asian (EAS) AF: 0.318 AC: 1643 AN: 5168

South Asian (SAS) AF: 0.416 AC: 2009 AN: 4824

European-Finnish (FIN) AF: 0.401 AC: 4244 AN: 10588

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21148 AN: 67962

Other (OTH) AF: 0.396 AC: 835 AN: 2108

Alfa AF: 0.350 Hom.: 5516

Bravo AF: 0.363

Asia WGS AF: 0.350 AC: 1218 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	7.6
DANN	Benign	0.65
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7775759; hg19: chr6-31352446;