chr15-39688081-C-G

Variant names:

• chr15-39688081-C-G
• rs2664124
• NM_152597.5:c.1188+25363G>C

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+25363G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,124 control chromosomes in the GnomAD database, including 51,784 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 (51784 hom., cov: 31)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 4 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=-0.93).
• 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+25363G>C		intron	N/A	NP_689810.3
	FSIP1	NM_001324338.2		c.1188+25363G>C		intron	N/A	NP_001311267.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP1	ENST00000350221.4	TSL:1 MANE Select	c.1188+25363G>C		intron	N/A	ENSP00000280236.3
	FSIP1	ENST00000884361.1		c.1188+25363G>C		intron	N/A	ENSP00000554420.1
	FSIP1	ENST00000942556.1		c.1029+25363G>C		intron	N/A	ENSP00000612615.1

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124594 AN: 152006 Hom.: 51739 Cov.: 31

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.820 AC: 124699 AN: 152124 Hom.: 51784 Cov.: 31 AF XY: 0.823 AC XY: 61225 AN XY: 74370

African (AFR) AF: 0.702 AC: 29138 AN: 41480

American (AMR) AF: 0.830 AC: 12692 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2852 AN: 3472

East Asian (EAS) AF: 0.602 AC: 3112 AN: 5166

South Asian (SAS) AF: 0.834 AC: 4019 AN: 4818

European-Finnish (FIN) AF: 0.907 AC: 9611 AN: 10596

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60514 AN: 67992

Other (OTH) AF: 0.813 AC: 1715 AN: 2110

Alfa AF: 0.861 Hom.: 3312

Bravo AF: 0.805

Asia WGS AF: 0.756 AC: 2629 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.70
PhyloP100		-1.6
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: rs2664124; hg19: chr15-39980282;