13-98308508-C-T

Variant names:

• chr13-98308508-C-T
• rs4318070
• NM_005766.4:c.172-35254C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005766.4(FARP1):​c.172-35254C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,066 control chromosomes in the GnomAD database, including 2,955 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 0.17 (2955 hom., cov: 31)
• Consequence: FARP1 NM_005766.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 8 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]

ENSG00000297447 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FARP1	NM_005766.4	c.172-35254C>T		intron_variant	Intron 2 of 26	ENST00000319562.11	NP_005757.1
FARP1	NM_001286839.2	c.172-35254C>T		intron_variant	Intron 2 of 27		NP_001273768.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FARP1	ENST00000319562.11	c.172-35254C>T		intron_variant	Intron 2 of 26	1	NM_005766.4	ENSP00000322926.6

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26253 AN: 151948 Hom.: 2958 Cov.: 31

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.173 AC: 26252 AN: 152066 Hom.: 2955 Cov.: 31 AF XY: 0.172 AC XY: 12748 AN XY: 74332

African (AFR) AF: 0.0490 AC: 2033 AN: 41522

American (AMR) AF: 0.145 AC: 2217 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3466

East Asian (EAS) AF: 0.0149 AC: 77 AN: 5176

South Asian (SAS) AF: 0.235 AC: 1129 AN: 4814

European-Finnish (FIN) AF: 0.215 AC: 2270 AN: 10554

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17084 AN: 67936

Other (OTH) AF: 0.164 AC: 346 AN: 2116

Alfa AF: 0.218 Hom.: 16889

Bravo AF: 0.157

Asia WGS AF: 0.112 AC: 391 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.67
DANN	Benign	0.70
PhyloP100		-1.5
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: rs4318070; hg19: chr13-98960762;