rs16969802

Variant names:

• chr15-39758161-T-C
• rs16969802
• NM_152597.5:c.559+5660A>G

Variant summary

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

The NM_152597.5(FSIP1):​c.559+5660A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 151,892 control chromosomes in the GnomAD database, including 4,820 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 0.24 (4820 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.559+5660A>G		intron_variant	Intron 5 of 11	ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.559+5660A>G		intron_variant	Intron 5 of 11	1	NM_152597.5	ENSP00000280236.3

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36827 AN: 151774 Hom.: 4818 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.243 AC: 36838 AN: 151892 Hom.: 4820 Cov.: 32 AF XY: 0.243 AC XY: 18071 AN XY: 74242

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.268

Alfa AF: 0.226 Hom.: 931

Bravo AF: 0.258

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.63

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: rs16969802; hg19: chr15-40050362;