Variant 6-31395153-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_148222.1(MICA-AS1):n.482G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 955,144 control chromosomes in the GnomAD database, including 56,944 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 0.40 ( 12824 hom., cov: 26)

Exomes 𝑓: 0.32 ( 44120 hom. )

Consequence

MICA-AS1
NR_148222.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05

Variant links:

Genes affected

ENSG00000272221 (HGNC:):

ENSG00000272221 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.06).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MICA-AS1	NR_148222.1 linkuse as main transcript	n.482G>A		non_coding_transcript_exon_variant	2/2
MICA-AS1	NR_148223.1 linkuse as main transcript	n.515G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000272221	ENST00000606743.1 linkuse as main transcript	n.343G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

58535

AN:

145622

Hom.:

12801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.515

Gnomad AMI

AF:

0.494

Gnomad AMR

AF:

0.480

Gnomad ASJ

AF:

0.630

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.394

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.477

Gnomad NFE

AF:

0.323

Gnomad OTH

AF:

0.456

GnomAD4 exome

AF:

0.315

AC:

255015

AN:

809406

Hom.:

44120

Cov.:

AF XY:

0.314

AC XY:

117319

AN XY:

373888

show subpopulations

Gnomad4 AFR exome

AF:

0.558

Gnomad4 AMR exome

AF:

0.551

Gnomad4 ASJ exome

AF:

0.629

Gnomad4 EAS exome

AF:

0.363

Gnomad4 SAS exome

AF:

0.399

Gnomad4 FIN exome

AF:

0.310

Gnomad4 NFE exome

AF:

0.303

Gnomad4 OTH exome

AF:

0.363

GnomAD4 genome

AF:

0.402

AC:

58609

AN:

145738

Hom.:

12824

Cov.:

AF XY:

0.402

AC XY:

28543

AN XY:

70934

show subpopulations

Gnomad4 AFR

AF:

0.515

Gnomad4 AMR

AF:

0.481

Gnomad4 ASJ

AF:

0.630

Gnomad4 EAS

AF:

0.331

Gnomad4 SAS

AF:

0.393

Gnomad4 FIN

AF:

0.315

Gnomad4 NFE

AF:

0.323

Gnomad4 OTH

AF:

0.459

Alfa

AF:

0.360

Hom.:

13372

Asia WGS

AF:

0.382

AC:

1326

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.94

DANN

Benign

0.28

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over