rs7179742

Positions:

• chr15-39770852-A-G

Variant summary

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

The NM_152597.5(FSIP1):​c.127-242T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,108 control chromosomes in the GnomAD database, including 15,069 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 0.43 (15069 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.127-242T>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.127-242T>C		intron_variant		1	NM_152597.5	ENSP00000280236	P1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66095 AN: 151990 Hom.: 15061 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.435 AC: 66136 AN: 152108 Hom.: 15069 Cov.: 32 AF XY: 0.435 AC XY: 32349 AN XY: 74354

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.429

Alfa AF: 0.475 Hom.: 17101

Bravo AF: 0.430

Asia WGS AF: 0.320 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
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: rs7179742; hg19: chr15-40063053;