13-98422309-A-G

Position:

• chr13-98422309-A-G

Variant summary

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

The NM_005766.4(FARP1):​c.1827-2263A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,076 control chromosomes in the GnomAD database, including 11,873 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 0.38 (11873 hom., cov: 32)
• Consequence: FARP1 NM_005766.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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]

FARP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FARP1	NM_005766.4	c.1827-2263A>G		intron_variant		ENST00000319562.11	NP_005757.1
FARP1	NM_001286839.2	c.1827-2263A>G		intron_variant			NP_001273768.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FARP1	ENST00000319562.11	c.1827-2263A>G		intron_variant		1	NM_005766.4	ENSP00000322926.6
FARP1	ENST00000595437.5	c.1827-2263A>G		intron_variant		1		ENSP00000471242.1
FARP1	ENST00000627049.2	c.1827-2263A>G		intron_variant		5		ENSP00000486285.1
FARP1	ENST00000457029.3	n.465-2263A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58141 AN: 151958 Hom.: 11844 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.383 AC: 58219 AN: 152076 Hom.: 11873 Cov.: 32 AF XY: 0.383 AC XY: 28443 AN XY: 74326

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.385

Alfa AF: 0.321 Hom.: 10501

Bravo AF: 0.398

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.78
DANN	Benign	0.35

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: rs7329659; hg19: chr13-99074563;