3-100006785-A-G

Variant names:

• chr3-100006785-A-G
• rs7649349
• NM_001387850.1:c.-10-75755T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387850.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FILIP1L	NM_001387850.1	MANE Select	c.-10-75755T>C		intron	N/A	NP_001374779.1
	CMSS1	NM_032359.4	MANE Select	c.65-140188A>G		intron	N/A	NP_115735.2
	FILIP1L	NM_182909.4		c.-10-75755T>C		intron	N/A	NP_878913.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FILIP1L	ENST00000477258.2	TSL:2 MANE Select	c.-10-75755T>C		intron	N/A	ENSP00000417617.2
	CMSS1	ENST00000421999.8	TSL:1 MANE Select	c.65-140188A>G		intron	N/A	ENSP00000410396.2
	FILIP1L	ENST00000354552.7	TSL:1	c.-10-75755T>C		intron	N/A	ENSP00000346560.3

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

African (AFR) AF: 0.548 AC: 22754 AN: 41498

American (AMR) AF: 0.572 AC: 8732 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3470

East Asian (EAS) AF: 0.725 AC: 3750 AN: 5174

South Asian (SAS) AF: 0.540 AC: 2606 AN: 4822

European-Finnish (FIN) AF: 0.580 AC: 6134 AN: 10574

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40496 AN: 67954

Other (OTH) AF: 0.595 AC: 1255 AN: 2110

Alfa AF: 0.596 Hom.: 4111

Bravo AF: 0.585

Asia WGS AF: 0.616 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		1.6
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: rs7649349; hg19: chr3-99725629;