NM_152597.5:c.560-311A>G

Variant names:

• chr15-39742211-T-C
• rs8031241
• NM_152597.5:c.560-311A>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.560-311A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,992 control chromosomes in the GnomAD database, including 24,099 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 0.56 (24099 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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.560-311A>G		intron	N/A	NP_689810.3
	FSIP1	NM_001324338.2		c.560-311A>G		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.560-311A>G		intron	N/A	ENSP00000280236.3
	FSIP1	ENST00000559692.1	TSL:3	n.147-311A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84958 AN: 151876 Hom.: 24077 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.559 AC: 85030 AN: 151992 Hom.: 24099 Cov.: 32 AF XY: 0.556 AC XY: 41311 AN XY: 74314

African (AFR) AF: 0.624 AC: 25842 AN: 41432

American (AMR) AF: 0.614 AC: 9378 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3470

East Asian (EAS) AF: 0.477 AC: 2466 AN: 5172

South Asian (SAS) AF: 0.417 AC: 2009 AN: 4812

European-Finnish (FIN) AF: 0.522 AC: 5511 AN: 10548

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36507 AN: 67970

Other (OTH) AF: 0.547 AC: 1150 AN: 2104

Alfa AF: 0.556 Hom.: 3568

Bravo AF: 0.572

Asia WGS AF: 0.479 AC: 1664 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.031
DANN	Benign	0.46
PhyloP100		-2.7
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: rs8031241; hg19: chr15-40034412;