3-99873752-C-T

Variant names:

• chr3-99873752-C-T
• rs813218
• NM_001387850.1:c.606-22682G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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]

LOC105374010 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FILIP1L	NM_001387850.1	c.606-22682G>A		intron_variant	Intron 4 of 5	ENST00000477258.2	NP_001374779.1
CMSS1	NM_032359.4	c.64+55709C>T		intron_variant	Intron 1 of 9	ENST00000421999.8	NP_115735.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FILIP1L	ENST00000477258.2	c.606-22682G>A		intron_variant	Intron 4 of 5	2	NM_001387850.1	ENSP00000417617.2
CMSS1	ENST00000421999.8	c.64+55709C>T		intron_variant	Intron 1 of 9	1	NM_032359.4	ENSP00000410396.2

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

African (AFR) AF: 0.595 AC: 24669 AN: 41444

American (AMR) AF: 0.485 AC: 7403 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1177 AN: 3468

East Asian (EAS) AF: 0.308 AC: 1592 AN: 5172

South Asian (SAS) AF: 0.531 AC: 2561 AN: 4822

European-Finnish (FIN) AF: 0.545 AC: 5735 AN: 10526

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32662 AN: 67916

Other (OTH) AF: 0.482 AC: 1017 AN: 2108

Alfa AF: 0.498 Hom.: 16072

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
PhyloP100		0.39
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs813218; hg19: chr3-99592596;