3-100006785-A-G

Position:

• chr3-100006785-A-G

Variant summary

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

The NM_001387850.1(FILIP1L):​c.-10-75755T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,068 control chromosomes in the GnomAD database, including 26,083 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 0.58 (26083 hom., cov: 33)
• Consequence: FILIP1L NM_001387850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63

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=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FILIP1L	NM_001387850.1	c.-10-75755T>C		intron_variant		ENST00000477258.2	NP_001374779.1
CMSS1	NM_032359.4	c.65-140188A>G		intron_variant		ENST00000421999.8	NP_115735.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CMSS1	ENST00000421999.8	c.65-140188A>G		intron_variant		1	NM_032359.4	ENSP00000410396	P1
FILIP1L	ENST00000477258.2	c.-10-75755T>C		intron_variant		2	NM_001387850.1	ENSP00000417617	P4

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88761 AN: 151950 Hom.: 26081 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.584 AC: 88794 AN: 152068 Hom.: 26083 Cov.: 33 AF XY: 0.582 AC XY: 43226 AN XY: 74326

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.595

Alfa AF: 0.597 Hom.: 3993

Bravo AF: 0.585

Asia WGS AF: 0.616 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.71

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: rs7649349; hg19: chr3-99725629;