15-39774154-C-T

Variant names:

• chr15-39774154-C-T
• rs1602543
• NM_152597.5:c.126+2245G>A

Variant summary

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

The NM_152597.5(FSIP1):​c.126+2245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,040 control chromosomes in the GnomAD database, including 1,834 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 0.12 (1834 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 1 publications found

Genes affected

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

ENSG00000259580 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP1	NM_152597.5	MANE Select	c.126+2245G>A		intron	N/A	NP_689810.3
	FSIP1	NM_001324338.2		c.126+2245G>A		intron	N/A	NP_001311267.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP1	ENST00000350221.4	TSL:1 MANE Select	c.126+2245G>A		intron	N/A	ENSP00000280236.3
	FSIP1	ENST00000884361.1		c.126+2245G>A		intron	N/A	ENSP00000554420.1
	FSIP1	ENST00000942556.1		c.126+2245G>A		intron	N/A	ENSP00000612615.1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18888 AN: 151922 Hom.: 1838 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0642

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0496

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.124 AC: 18898 AN: 152040 Hom.: 1834 Cov.: 32 AF XY: 0.125 AC XY: 9258 AN XY: 74306

African (AFR) AF: 0.261 AC: 10801 AN: 41430

American (AMR) AF: 0.104 AC: 1588 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3472

East Asian (EAS) AF: 0.248 AC: 1283 AN: 5172

South Asian (SAS) AF: 0.126 AC: 609 AN: 4818

European-Finnish (FIN) AF: 0.0642 AC: 679 AN: 10578

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0496 AC: 3370 AN: 67984

Other (OTH) AF: 0.115 AC: 242 AN: 2112

Alfa AF: 0.0909 Hom.: 175

Bravo AF: 0.133

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.76
PhyloP100		0.10
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: rs1602543; hg19: chr15-40066355;