chr6-31386818-T-C

Variant names:

• chr6-31386818-T-C
• rs2596562
• ENST00000745027.1:n.568-3628A>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.568-3628A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,980 control chromosomes in the GnomAD database, including 14,055 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 0.42 (14055 hom., cov: 31)
• Consequence: MICA-AS1 ENST00000745027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901300	XR_007059542.1	n.75-445T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICA-AS1	ENST00000745027.1	n.568-3628A>G		intron_variant	Intron 1 of 1
MICA-AS1	ENST00000745028.1	n.330+24A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63545 AN: 151862 Hom.: 14032 Cov.: 31

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.419 AC: 63623 AN: 151980 Hom.: 14055 Cov.: 31 AF XY: 0.420 AC XY: 31175 AN XY: 74280

African (AFR) AF: 0.536 AC: 22197 AN: 41420

American (AMR) AF: 0.507 AC: 7739 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2211 AN: 3472

East Asian (EAS) AF: 0.354 AC: 1828 AN: 5164

South Asian (SAS) AF: 0.410 AC: 1974 AN: 4818

European-Finnish (FIN) AF: 0.345 AC: 3642 AN: 10552

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22429 AN: 67962

Other (OTH) AF: 0.479 AC: 1011 AN: 2112

Alfa AF: 0.380 Hom.: 10852

Bravo AF: 0.440

Asia WGS AF: 0.398 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.28
PhyloP100		-3.2

Splicing

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

Publications

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Other links and lift over

dbSNP: rs2596562; hg19: chr6-31354595;