15-39651442-T-C

Variant names:

• chr15-39651442-T-C
• rs10520144
• NM_152597.5:c.1189-33197A>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.1189-33197A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0256 in 152,308 control chromosomes in the GnomAD database, including 152 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 0.026 (152 hom., cov: 33)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.1189-33197A>G		intron_variant	Intron 10 of 11	ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.1189-33197A>G		intron_variant	Intron 10 of 11	1	NM_152597.5	ENSP00000280236.3

Frequencies

GnomAD3 genomes AF: 0.0257 AC: 3907 AN: 152190 Hom.: 153 Cov.: 33

Gnomad AFR AF: 0.00487

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0209

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0807

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.0206

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

GnomAD4 genome AF: 0.0256 AC: 3902 AN: 152308 Hom.: 152 Cov.: 33 AF XY: 0.0322 AC XY: 2399 AN XY: 74470

African (AFR) AF: 0.00486 AC: 202 AN: 41568

American (AMR) AF: 0.0209 AC: 320 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3470

East Asian (EAS) AF: 0.104 AC: 542 AN: 5190

South Asian (SAS) AF: 0.0806 AC: 389 AN: 4826

European-Finnish (FIN) AF: 0.126 AC: 1332 AN: 10606

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0148 AC: 1007 AN: 68038

Other (OTH) AF: 0.0204 AC: 43 AN: 2108

Alfa AF: 0.0202 Hom.: 6

Bravo AF: 0.0171

Asia WGS AF: 0.105 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.65
PhyloP100		0.90
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: rs10520144; hg19: chr15-39943643;