13-98179341-C-G

Position:

• chr13-98179341-C-G

Variant summary

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

The NM_005766.4(FARP1):​c.-23-33879C>G 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 152,056 control chromosomes in the GnomAD database, including 26,231 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 (26231 hom., cov: 32)
• Consequence: FARP1 NM_005766.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FARP1	NM_005766.4	c.-23-33879C>G		intron_variant		ENST00000319562.11	NP_005757.1
FARP1	NM_001001715.4	c.-23-33879C>G		intron_variant			NP_001001715.2
FARP1	NM_001286839.2	c.-23-33879C>G		intron_variant			NP_001273768.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FARP1	ENST00000319562.11	c.-23-33879C>G		intron_variant		1	NM_005766.4	ENSP00000322926	P1

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88778 AN: 151938 Hom.: 26224 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.584 AC: 88822 AN: 152056 Hom.: 26231 Cov.: 32 AF XY: 0.584 AC XY: 43399 AN XY: 74328

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.602

Alfa AF: 0.471 Hom.: 1321

Bravo AF: 0.577

Asia WGS AF: 0.602 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs9556893; hg19: chr13-98831595;