dbSNP rs10423723: ENSG00000285526:c.-393C>T (chr19-35106716-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000648240(ENSG00000285526):c.-393C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 455,978 control chromosomes in the GnomAD database, including 46,116 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 0.48 ( 17878 hom., cov: 32)

Exomes 𝑓: 0.43 ( 28238 hom. )

Consequence

ENSG00000285526
ENST00000648240 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

Variant links:

Genes affected

ENSG00000285526 (HGNC:):

ENSG00000285526 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=-0.63).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904701	XM_047439795.1 link	c.*798C>T		3_prime_UTR_variant	Exon 2 of 2		XP_047295751.1
LOC124904701	XR_007067238.1 link	n.2391C>T		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285526	ENST00000648240 link	c.-393C>T		5_prime_UTR_variant	Exon 1 of 9			ENSP00000497169.1

Frequencies

GnomAD3 genomes

AF:

0.476

AC:

72274

AN:

151884

Hom.:

17861

Cov.:

show subpopulations

Gnomad AFR

AF:

0.608

Gnomad AMI

AF:

0.272

Gnomad AMR

AF:

0.452

Gnomad ASJ

AF:

0.439

Gnomad EAS

AF:

0.448

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.373

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.429

Gnomad OTH

AF:

0.459

GnomAD3 exomes

AF:

0.431

AC:

55349

AN:

128418

Hom.:

12136

AF XY:

0.427

AC XY:

30005

AN XY:

70326

show subpopulations

Gnomad AFR exome

AF:

0.604

Gnomad AMR exome

AF:

0.429

Gnomad ASJ exome

AF:

0.448

Gnomad EAS exome

AF:

0.451

Gnomad SAS exome

AF:

0.394

Gnomad FIN exome

AF:

0.379

Gnomad NFE exome

AF:

0.427

Gnomad OTH exome

AF:

0.414

GnomAD4 exome

AF:

0.428

AC:

130124

AN:

303976

Hom.:

28238

Cov.:

AF XY:

0.424

AC XY:

73369

AN XY:

173082

show subpopulations

Gnomad4 AFR exome

AF:

0.604

Gnomad4 AMR exome

AF:

0.428

Gnomad4 ASJ exome

AF:

0.442

Gnomad4 EAS exome

AF:

0.440

Gnomad4 SAS exome

AF:

0.405

Gnomad4 FIN exome

AF:

0.382

Gnomad4 NFE exome

AF:

0.428

Gnomad4 OTH exome

AF:

0.442

GnomAD4 genome

AF:

0.476

AC:

72327

AN:

152002

Hom.:

17878

Cov.:

AF XY:

0.473

AC XY:

35165

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.608

Gnomad4 AMR

AF:

0.452

Gnomad4 ASJ

AF:

0.439

Gnomad4 EAS

AF:

0.447

Gnomad4 SAS

AF:

0.408

Gnomad4 FIN

AF:

0.373

Gnomad4 NFE

AF:

0.429

Gnomad4 OTH

AF:

0.455

Alfa

AF:

0.433

Hom.:

16923

Bravo

AF:

0.484

Asia WGS

AF:

0.427

AC:

1483

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

2.3

DANN

Benign

0.94

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