Genetic Variant ENSG00000231188:n.103+1524G>A (chr10-100344764-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000429420.1(ENSG00000231188):n.103+1524G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 501,206 control chromosomes in the GnomAD database, including 44,382 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 0.45 ( 16291 hom., cov: 32)

Exomes 𝑓: 0.39 ( 28091 hom. )

Consequence

ENSG00000231188
ENST00000429420.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27

Variant links:

Genes affected

ENSG00000231188 (HGNC:):

ENSG00000231188 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231188	ENST00000429420.1 link	n.103+1524G>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.452

AC:

68592

AN:

151692

Hom.:

16275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.607

Gnomad AMI

AF:

0.472

Gnomad AMR

AF:

0.383

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.382

Gnomad SAS

AF:

0.465

Gnomad FIN

AF:

0.460

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.383

Gnomad OTH

AF:

0.435

GnomAD3 exomes

AF:

0.393

AC:

86185

AN:

219426

Hom.:

17676

AF XY:

0.397

AC XY:

48175

AN XY:

121404

show subpopulations

Gnomad AFR exome

AF:

0.599

Gnomad AMR exome

AF:

0.312

Gnomad ASJ exome

AF:

0.337

Gnomad EAS exome

AF:

0.347

Gnomad SAS exome

AF:

0.453

Gnomad FIN exome

AF:

0.458

Gnomad NFE exome

AF:

0.381

Gnomad OTH exome

AF:

0.384

GnomAD4 exome

AF:

0.392

AC:

137027

AN:

349396

Hom.:

28091

Cov.:

AF XY:

0.399

AC XY:

79972

AN XY:

200478

show subpopulations

Gnomad4 AFR exome

AF:

0.586

Gnomad4 AMR exome

AF:

0.317

Gnomad4 ASJ exome

AF:

0.331

Gnomad4 EAS exome

AF:

0.339

Gnomad4 SAS exome

AF:

0.452

Gnomad4 FIN exome

AF:

0.445

Gnomad4 NFE exome

AF:

0.378

Gnomad4 OTH exome

AF:

0.396

GnomAD4 genome

AF:

0.452

AC:

68653

AN:

151810

Hom.:

16291

Cov.:

AF XY:

0.457

AC XY:

33883

AN XY:

74178

show subpopulations

Gnomad4 AFR

AF:

0.607

Gnomad4 AMR

AF:

0.382

Gnomad4 ASJ

AF:

0.342

Gnomad4 EAS

AF:

0.382

Gnomad4 SAS

AF:

0.467

Gnomad4 FIN

AF:

0.460

Gnomad4 NFE

AF:

0.383

Gnomad4 OTH

AF:

0.435

Alfa

AF:

0.391

Hom.:

28562

Bravo

AF:

0.447

Asia WGS

AF:

0.438

AC:

1524

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.20

DANN

Benign

0.61

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