rs813218

chr3-99873752-C-T

Variant summary

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

The NM_001387850.1(FILIP1L):c.606-22682G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,924 control chromosomes in the GnomAD database, including 20,195 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 (20195 hom., cov: 32)
• Consequence: FILIP1L NM_001387850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387

Genes affected

FILIP1L (HGNC:24589): (filamin A interacting protein 1 like) Predicted to be located in cytoplasm; membrane; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

CMSS1 (HGNC:28666): (cms1 ribosomal small subunit homolog) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FILIP1L	NM_001387850.1	c.606-22682G>A		intron_variant		ENST00000477258.2
CMSS1	NM_032359.4	c.64+55709C>T		intron_variant		ENST00000421999.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMSS1	ENST00000421999.8	c.64+55709C>T		intron_variant		1	NM_032359.4	P1
FILIP1L	ENST00000477258.2	c.606-22682G>A		intron_variant		2	NM_001387850.1	P4

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77370 AN: 151804 Hom.: 20161 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.510 AC: 77458 AN: 151924 Hom.: 20195 Cov.: 32 AF XY: 0.512 AC XY: 37975 AN XY: 74238

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.482

Alfa AF: 0.485 Hom.: 9863

Bravo AF: 0.505

Asia WGS AF: 0.446 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	5.3
Dann	Benign	0.33

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: rs813218; hg19: chr3-99592596;