rs12440567

Positions:

• chr15-39767334-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152597.5(FSIP1):​c.311-1588C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,100 control chromosomes in the GnomAD database, including 1,797 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 0.14 (1797 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FSIP1	NM_152597.5	c.311-1588C>T		intron_variant		ENST00000350221.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSIP1	ENST00000350221.4	c.311-1588C>T		intron_variant		1	NM_152597.5	P1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20946 AN: 151980 Hom.: 1791 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.138 AC: 20965 AN: 152100 Hom.: 1797 Cov.: 32 AF XY: 0.143 AC XY: 10614 AN XY: 74354

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.145

Alfa AF: 0.149 Hom.: 395

Bravo AF: 0.146

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.9
DANN	Benign	0.74

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

Publications

LitVar

Other links and lift over

dbSNP: rs12440567; hg19: chr15-40059535;