chr15-39745559-T-G

Position:

• chr15-39745559-T-G

Variant summary

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

The NM_152597.5(FSIP1):​c.560-3659A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,120 control chromosomes in the GnomAD database, including 3,844 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 0.18 (3844 hom., cov: 31)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.560-3659A>C		intron_variant		ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.560-3659A>C		intron_variant		1	NM_152597.5	ENSP00000280236	P1
FSIP1	ENST00000559692.1	n.146+1743A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28054 AN: 152002 Hom.: 3834 Cov.: 31

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0688

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.185 AC: 28102 AN: 152120 Hom.: 3844 Cov.: 31 AF XY: 0.193 AC XY: 14328 AN XY: 74372

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.0688

Gnomad4 OTH AF: 0.174

Alfa AF: 0.132 Hom.: 266

Bravo AF: 0.203

Asia WGS AF: 0.340 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.23

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: rs6492915; hg19: chr15-40037760;