13-98341776-A-G

Variant names:

• chr13-98341776-A-G
• rs9584805
• NM_005766.4:c.172-1986A>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.172-1986A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,170 control chromosomes in the GnomAD database, including 8,902 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 0.33 (8902 hom., cov: 33)
• Consequence: FARP1 NM_005766.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 7 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 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.172-1986A>G		intron	N/A	NP_005757.1
	FARP1	NM_001286839.2		c.172-1986A>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.172-1986A>G		intron	N/A	ENSP00000322926.6
	FARP1	ENST00000595437.5	TSL:1	c.172-1986A>G		intron	N/A	ENSP00000471242.1
	FARP1	ENST00000627049.2	TSL:5	c.172-1986A>G		intron	N/A	ENSP00000486285.1

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49588 AN: 152052 Hom.: 8891 Cov.: 33

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.326 AC: 49636 AN: 152170 Hom.: 8902 Cov.: 33 AF XY: 0.316 AC XY: 23528 AN XY: 74374

African (AFR) AF: 0.453 AC: 18817 AN: 41496

American (AMR) AF: 0.223 AC: 3412 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3472

East Asian (EAS) AF: 0.0187 AC: 97 AN: 5182

South Asian (SAS) AF: 0.226 AC: 1093 AN: 4826

European-Finnish (FIN) AF: 0.226 AC: 2392 AN: 10586

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21763 AN: 67996

Other (OTH) AF: 0.299 AC: 630 AN: 2108

Alfa AF: 0.314 Hom.: 28193

Bravo AF: 0.325

Asia WGS AF: 0.143 AC: 500 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.0
DANN	Benign	0.46
PhyloP100		-0.18
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: rs9584805; hg19: chr13-98994030;