rs1906164

Positions:

• chr15-39740548-C-T

Variant summary

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

The NM_152597.5(FSIP1):​c.656-759G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,922 control chromosomes in the GnomAD database, including 20,773 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 0.51 (20773 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FSIP1	NM_152597.5	c.656-759G>A		intron_variant		ENST00000350221.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSIP1	ENST00000350221.4	c.656-759G>A		intron_variant		1	NM_152597.5	P1
FSIP1	ENST00000559692.1	n.243-759G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77870 AN: 151806 Hom.: 20756 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.513 AC: 77927 AN: 151922 Hom.: 20773 Cov.: 32 AF XY: 0.505 AC XY: 37458 AN XY: 74218

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.492

Alfa AF: 0.514 Hom.: 5234

Bravo AF: 0.514

Asia WGS AF: 0.312 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.41
DANN	Benign	0.32

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: rs1906164; hg19: chr15-40032749;