rs688872

Positions:

• chr13-98314063-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.172-29699A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,020 control chromosomes in the GnomAD database, including 35,486 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 0.68 (35486 hom., cov: 31)
• Consequence: FARP1 NM_005766.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FARP1	NM_005766.4	c.172-29699A>G		intron_variant		ENST00000319562.11	NP_005757.1
FARP1	NM_001286839.2	c.172-29699A>G		intron_variant			NP_001273768.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FARP1	ENST00000319562.11	c.172-29699A>G		intron_variant		1	NM_005766.4	ENSP00000322926.6

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103572 AN: 151902 Hom.: 35444 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.682 AC: 103670 AN: 152020 Hom.: 35486 Cov.: 31 AF XY: 0.686 AC XY: 50978 AN XY: 74300

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.672

Alfa AF: 0.658 Hom.: 46037

Bravo AF: 0.677

Asia WGS AF: 0.727 AC: 2528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.16

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: rs688872; hg19: chr13-98966317;