rs2998394

chr6-75447650-C-A

Variant summary

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

The NM_015687.5(FILIP1):c.-6-32672G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 151,990 control chromosomes in the GnomAD database, including 37,890 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 0.70 (37890 hom., cov: 32)
• Consequence: FILIP1 NM_015687.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

FILIP1 (HGNC:21015): (filamin A interacting protein 1) This gene encodes a filamin A binding protein. The encoded protein promotes the degradation of filamin A and may regulate cortical neuron migration and dendritic spine morphology. Mice lacking a functional copy of this gene exhibit reduced dendritic spine length and altered excitatory signaling. [provided by RefSeq, Oct 2016]

LOC101928540 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FILIP1	NM_015687.5	c.-6-32672G>T		intron_variant		ENST00000237172.12
LOC101928540	NR_125859.1	n.209-5346C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FILIP1	ENST00000237172.12	c.-6-32672G>T		intron_variant		1	NM_015687.5	P4
FILIP1	ENST00000393004.6	c.-6-32672G>T		intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105936 AN: 151870 Hom.: 37853 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.698 AC: 106016 AN: 151990 Hom.: 37890 Cov.: 32 AF XY: 0.692 AC XY: 51448 AN XY: 74300

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.659

Alfa AF: 0.680 Hom.: 4475

Bravo AF: 0.699

Asia WGS AF: 0.629 AC: 2190 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.096
Dann	Benign	0.49

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: rs2998394; hg19: chr6-76157366;