13-98422309-A-G

Variant names:

• chr13-98422309-A-G
• rs7329659
• NM_005766.4:c.1827-2263A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005766.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FARP1	NM_005766.4	MANE Select	c.1827-2263A>G		intron	N/A	NP_005757.1
	FARP1	NM_001286839.2		c.1827-2263A>G		intron	N/A	NP_001273768.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FARP1	ENST00000319562.11	TSL:1 MANE Select	c.1827-2263A>G		intron	N/A	ENSP00000322926.6
	FARP1	ENST00000595437.5	TSL:1	c.1827-2263A>G		intron	N/A	ENSP00000471242.1
	FARP1	ENST00000627049.2	TSL:5	c.1827-2263A>G		intron	N/A	ENSP00000486285.1

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

African (AFR) AF: 0.524 AC: 21699 AN: 41446

American (AMR) AF: 0.434 AC: 6635 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 869 AN: 3472

East Asian (EAS) AF: 0.321 AC: 1659 AN: 5170

South Asian (SAS) AF: 0.403 AC: 1938 AN: 4812

European-Finnish (FIN) AF: 0.275 AC: 2918 AN: 10594

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21286 AN: 67980

Other (OTH) AF: 0.385 AC: 813 AN: 2110

Alfa AF: 0.345 Hom.: 18092

Bravo AF: 0.398

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.78
DANN	Benign	0.35
PhyloP100		-1.0
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: rs7329659; hg19: chr13-99074563;