13-98179341-C-G

Variant names:

• chr13-98179341-C-G
• rs9556893
• NM_005766.4:c.-23-33879C>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.-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
• Publications: 2 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FARP1	NM_005766.4	MANE Select	c.-23-33879C>G		intron	N/A	NP_005757.1	A0A2X0TVY0
	FARP1	NM_001286839.2		c.-23-33879C>G		intron	N/A	NP_001273768.1	C9JME2
	FARP1	NM_001001715.4		c.-23-33879C>G		intron	N/A	NP_001001715.2	Q9Y4F1-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FARP1	ENST00000319562.11	TSL:1 MANE Select	c.-23-33879C>G		intron	N/A	ENSP00000322926.6	Q9Y4F1-1
	FARP1	ENST00000595437.5	TSL:1	c.-23-33879C>G		intron	N/A	ENSP00000471242.1	C9JME2
	FARP1	ENST00000871505.1		c.-23-33879C>G		intron	N/A	ENSP00000541564.1

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

African (AFR) AF: 0.508 AC: 21054 AN: 41472

American (AMR) AF: 0.564 AC: 8617 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2161 AN: 3470

East Asian (EAS) AF: 0.673 AC: 3485 AN: 5176

South Asian (SAS) AF: 0.654 AC: 3155 AN: 4822

European-Finnish (FIN) AF: 0.648 AC: 6839 AN: 10562

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41523 AN: 67960

Other (OTH) AF: 0.602 AC: 1271 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.48
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9556893; hg19: chr13-98831595;