15-39769885-T-C

Position:

• chr15-39769885-T-C

Variant summary

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

The NM_152597.5(FSIP1):​c.310+542A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,042 control chromosomes in the GnomAD database, including 14,476 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 0.42 (14476 hom., cov: 31)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.310+542A>G		intron_variant		ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.310+542A>G		intron_variant		1	NM_152597.5	ENSP00000280236	P1

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64228 AN: 151922 Hom.: 14462 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.423 AC: 64285 AN: 152042 Hom.: 14476 Cov.: 31 AF XY: 0.423 AC XY: 31467 AN XY: 74324

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.416

Alfa AF: 0.348 Hom.: 1534

Bravo AF: 0.416

Asia WGS AF: 0.311 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.70

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: rs1021411; hg19: chr15-40062086;