15-39685932-T-C

Variant names:

• chr15-39685932-T-C
• rs2412424
• NM_152597.5:c.1188+27512A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152597.5(FSIP1):​c.1188+27512A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,116 control chromosomes in the GnomAD database, including 53,346 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 0.83 (53346 hom., cov: 31)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152597.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP1	NM_152597.5	MANE Select	c.1188+27512A>G		intron	N/A	NP_689810.3
	FSIP1	NM_001324338.2		c.1188+27512A>G		intron	N/A	NP_001311267.1	Q8NA03

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP1	ENST00000350221.4	TSL:1 MANE Select	c.1188+27512A>G		intron	N/A	ENSP00000280236.3	Q8NA03
	FSIP1	ENST00000884361.1		c.1188+27512A>G		intron	N/A	ENSP00000554420.1
	FSIP1	ENST00000942556.1		c.1029+27512A>G		intron	N/A	ENSP00000612615.1

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126710 AN: 152000 Hom.: 53297 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.834 AC: 126820 AN: 152116 Hom.: 53346 Cov.: 31 AF XY: 0.836 AC XY: 62199 AN XY: 74380

African (AFR) AF: 0.751 AC: 31134 AN: 41452

American (AMR) AF: 0.836 AC: 12774 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2853 AN: 3472

East Asian (EAS) AF: 0.603 AC: 3115 AN: 5166

South Asian (SAS) AF: 0.834 AC: 4017 AN: 4816

European-Finnish (FIN) AF: 0.906 AC: 9599 AN: 10594

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60538 AN: 68016

Other (OTH) AF: 0.825 AC: 1740 AN: 2108

Alfa AF: 0.866 Hom.: 7508

Bravo AF: 0.821

Asia WGS AF: 0.759 AC: 2639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.37
PhyloP100		-0.52
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2412424; hg19: chr15-39978133;