13-98443780-A-G

Variant names:

• chr13-98443780-A-G
• rs9517302
• NM_005766.4:c.2797-2318A>G

Variant summary

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

The NM_005766.4(FARP1):​c.2797-2318A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 151,994 control chromosomes in the GnomAD database, including 40,635 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 0.72 (40635 hom., cov: 31)
• Consequence: FARP1 NM_005766.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

Genes affected

FARP1 (HGNC:3591): (FERM, ARH/RhoGEF and pleckstrin domain protein 1) This gene encodes a protein containing a FERM (4.2, exrin, radixin, moesin) domain, a Dbl homology domain, and two pleckstrin homology domains. These domains are found in guanine nucleotide exchange factors and proteins that link the cytoskeleton to the cell membrane. The encoded protein functions in neurons to promote dendritic growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FARP1	NM_005766.4	c.2797-2318A>G		intron_variant	Intron 24 of 26	ENST00000319562.11	NP_005757.1
FARP1	NM_001286839.2	c.2890-2318A>G		intron_variant	Intron 25 of 27		NP_001273768.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FARP1	ENST00000319562.11	c.2797-2318A>G		intron_variant	Intron 24 of 26	1	NM_005766.4	ENSP00000322926.6
FARP1	ENST00000595437.5	c.2890-2318A>G		intron_variant	Intron 25 of 27	1		ENSP00000471242.1
FARP1	ENST00000627049.2	c.2890-2318A>G		intron_variant	Intron 25 of 27	5		ENSP00000486285.1

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109850 AN: 151876 Hom.: 40619 Cov.: 31

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.723 AC: 109897 AN: 151994 Hom.: 40635 Cov.: 31 AF XY: 0.722 AC XY: 53654 AN XY: 74272

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.722

Alfa AF: 0.787 Hom.: 94439

Bravo AF: 0.706

Asia WGS AF: 0.649 AC: 2256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.67

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: rs9517302; hg19: chr13-99096034;