15-39700464-T-C

Position:

• chr15-39700464-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152597.5(FSIP1):​c.1188+12980A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 152,220 control chromosomes in the GnomAD database, including 51,011 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 0.82 (51011 hom., cov: 33)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.1188+12980A>G		intron_variant		ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.1188+12980A>G		intron_variant		1	NM_152597.5	ENSP00000280236.3

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123978 AN: 152102 Hom.: 50973 Cov.: 33

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.797

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.815 AC: 124075 AN: 152220 Hom.: 51011 Cov.: 33 AF XY: 0.819 AC XY: 60956 AN XY: 74422

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.903

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.795

Alfa AF: 0.853 Hom.: 15251

Bravo AF: 0.801

Asia WGS AF: 0.745 AC: 2590 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.59

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

Other links and lift over

dbSNP: rs2254829; hg19: chr15-39992665;