Variant chr15-39770624-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_152597.5(FSIP1):c.127-14G>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 1,373,862 control chromosomes in the GnomAD database, including 82,689 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7717 hom., cov: 32)

Exomes 𝑓: 0.35 ( 74972 hom. )

Consequence

FSIP1
NM_152597.5 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0680

Variant links:

Genes affected

FSIP1 (HGNC:21674): (fibrous sheath interacting protein 1)

FSIP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 15-39770624-C-A is Benign according to our data. Variant chr15-39770624-C-A is described in ClinVar as [Benign]. Clinvar id is 402884.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSIP1	NM_152597.5 linkuse as main transcript	c.127-14G>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4 linkuse as main transcript	c.127-14G>T		splice_polypyrimidine_tract_variant, intron_variant		1	NM_152597.5	ENSP00000280236	P1

Frequencies

GnomAD3 genomes

AF:

0.303

AC:

45172

AN:

149030

Hom.:

7707

Cov.:

show subpopulations

Gnomad AFR

AF:

0.130

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.421

Gnomad ASJ

AF:

0.304

Gnomad EAS

AF:

0.238

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.437

Gnomad MID

AF:

0.236

Gnomad NFE

AF:

0.367

Gnomad OTH

AF:

0.301

GnomAD3 exomes

AF:

0.386

AC:

49117

AN:

127340

Hom.:

8144

AF XY:

0.388

AC XY:

27027

AN XY:

69678

show subpopulations

Gnomad AFR exome

AF:

0.150

Gnomad AMR exome

AF:

0.537

Gnomad ASJ exome

AF:

0.371

Gnomad EAS exome

AF:

0.306

Gnomad SAS exome

AF:

0.331

Gnomad FIN exome

AF:

0.456

Gnomad NFE exome

AF:

0.397

Gnomad OTH exome

AF:

0.409

GnomAD4 exome

AF:

0.355

AC:

434437

AN:

1224726

Hom.:

74972

Cov.:

AF XY:

0.353

AC XY:

211597

AN XY:

599420

show subpopulations

Gnomad4 AFR exome

AF:

0.113

Gnomad4 AMR exome

AF:

0.493

Gnomad4 ASJ exome

AF:

0.313

Gnomad4 EAS exome

AF:

0.299

Gnomad4 SAS exome

AF:

0.267

Gnomad4 FIN exome

AF:

0.431

Gnomad4 NFE exome

AF:

0.363

Gnomad4 OTH exome

AF:

0.343

GnomAD4 genome

AF:

0.303

AC:

45209

AN:

149136

Hom.:

7717

Cov.:

AF XY:

0.309

AC XY:

22524

AN XY:

72842

show subpopulations

Gnomad4 AFR

AF:

0.131

Gnomad4 AMR

AF:

0.422

Gnomad4 ASJ

AF:

0.304

Gnomad4 EAS

AF:

0.238

Gnomad4 SAS

AF:

0.265

Gnomad4 FIN

AF:

0.437

Gnomad4 NFE

AF:

0.367

Gnomad4 OTH

AF:

0.304

Alfa

AF:

0.199

Hom.:

338

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

2.1

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over