Variant rs1240373 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000444431.1(ENSG00000151303):n.1152C>G 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 0.348 in 1,021,504 control chromosomes in the GnomAD database, including 66,073 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 0.43 ( 15655 hom., cov: 32)

Exomes 𝑓: 0.33 ( 50418 hom. )

Consequence

ENSG00000151303
ENST00000444431.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.117

Variant links:

Genes affected

ENSG00000151303 (HGNC:):

ENSG00000151303 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BMS1P3	use as main transcript	n.87000265C>G		intragenic_variant
AGAP11	NR_171046.1 linkuse as main transcript	n.1306-54C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
ENSG00000151303	ENST00000444431.1 linkuse as main transcript	n.1152C>G	non_coding_transcript_exon_variant	4/7	1
BMS1P3	ENST00000372011.4 linkuse as main transcript	n.816-54C>G	intron_variant		6
ENSG00000271880	ENST00000433214.2 linkuse as main transcript	n.1002-54C>G	intron_variant		2
ENSG00000272508	ENST00000444180.3 linkuse as main transcript	n.345-54C>G	intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.431

AC:

65459

AN:

151826

Hom.:

15617

Cov.:

show subpopulations

Gnomad AFR

AF:

0.639

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.492

Gnomad ASJ

AF:

0.403

Gnomad EAS

AF:

0.244

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.335

Gnomad OTH

AF:

0.403

GnomAD4 exome

AF:

0.333

AC:

289761

AN:

869560

Hom.:

50418

Cov.:

AF XY:

0.335

AC XY:

143952

AN XY:

430108

show subpopulations

Gnomad4 AFR exome

AF:

0.646

Gnomad4 AMR exome

AF:

0.554

Gnomad4 ASJ exome

AF:

0.398

Gnomad4 EAS exome

AF:

0.235

Gnomad4 SAS exome

AF:

0.352

Gnomad4 FIN exome

AF:

0.310

Gnomad4 NFE exome

AF:

0.321

Gnomad4 OTH exome

AF:

0.345

GnomAD4 genome

AF:

0.431

AC:

65543

AN:

151944

Hom.:

15655

Cov.:

AF XY:

0.428

AC XY:

31824

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.639

Gnomad4 AMR

AF:

0.492

Gnomad4 ASJ

AF:

0.403

Gnomad4 EAS

AF:

0.244

Gnomad4 SAS

AF:

0.353

Gnomad4 FIN

AF:

0.312

Gnomad4 NFE

AF:

0.335

Gnomad4 OTH

AF:

0.401

Alfa

AF:

0.216

Hom.:

436

Bravo

AF:

0.452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

5.1

DANN

Benign

0.20

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