6-31383258-T-C

Variant names:

• chr6-31383258-T-C
• rs2523485
• ENST00000745027.1:n.568-68A>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.568-68A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,260 control chromosomes in the GnomAD database, including 58,322 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 0.87 (58322 hom., cov: 32)
• Consequence: MICA-AS1 ENST00000745027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 10 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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.568-68A>G		intron	N/A
	MICA-AS1	ENST00000745028.1		n.331-68A>G		intron	N/A
	MICA-AS1	ENST00000745029.1		n.233-68A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.874 AC: 133019 AN: 152142 Hom.: 58267 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.954

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.874 AC: 133131 AN: 152260 Hom.: 58322 Cov.: 32 AF XY: 0.878 AC XY: 65383 AN XY: 74430

African (AFR) AF: 0.865 AC: 35921 AN: 41534

American (AMR) AF: 0.911 AC: 13945 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3324 AN: 3472

East Asian (EAS) AF: 0.972 AC: 5043 AN: 5188

South Asian (SAS) AF: 0.954 AC: 4599 AN: 4820

European-Finnish (FIN) AF: 0.872 AC: 9241 AN: 10594

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58018 AN: 68028

Other (OTH) AF: 0.902 AC: 1906 AN: 2112

Alfa AF: 0.864 Hom.: 109504

Bravo AF: 0.876

Asia WGS AF: 0.947 AC: 3295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.0
DANN	Benign	0.29
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2523485; hg19: chr6-31351035;