rs1021341

Variant names:

• chr3-100067445-A-G
• rs1021341
• NM_001387850.1:c.-11+46608T>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.-11+46608T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,094 control chromosomes in the GnomAD database, including 3,526 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 0.21 (3526 hom., cov: 31)
• Consequence: FILIP1L NM_001387850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 5 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FILIP1L	NM_001387850.1	c.-11+46608T>C		intron_variant	Intron 1 of 5	ENST00000477258.2	NP_001374779.1
CMSS1	NM_032359.4	c.65-79528A>G		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.-11+46608T>C		intron_variant	Intron 1 of 5	2	NM_001387850.1	ENSP00000417617.2
CMSS1	ENST00000421999.8	c.65-79528A>G		intron_variant	Intron 1 of 9	1	NM_032359.4	ENSP00000410396.2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32062 AN: 151976 Hom.: 3523 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.211 AC: 32106 AN: 152094 Hom.: 3526 Cov.: 31 AF XY: 0.214 AC XY: 15897 AN XY: 74356

African (AFR) AF: 0.161 AC: 6692 AN: 41502

American (AMR) AF: 0.241 AC: 3681 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3464

East Asian (EAS) AF: 0.158 AC: 816 AN: 5178

South Asian (SAS) AF: 0.258 AC: 1243 AN: 4812

European-Finnish (FIN) AF: 0.246 AC: 2597 AN: 10566

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15493 AN: 67978

Other (OTH) AF: 0.209 AC: 440 AN: 2108

Alfa AF: 0.220 Hom.: 4812

Bravo AF: 0.208

Asia WGS AF: 0.204 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.52
PhyloP100		-0.030
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: rs1021341; hg19: chr3-99786289;