NM_005766.4:c.172-29699A>G

Variant names:

• chr13-98314063-A-G
• rs688872
• NM_005766.4:c.172-29699A>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.172-29699A>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
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.715 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.172-29699A>G		intron	N/A	NP_005757.1
	FARP1	NM_001286839.2		c.172-29699A>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.172-29699A>G		intron	N/A	ENSP00000322926.6
	FARP1	ENST00000595437.5	TSL:1	c.172-29699A>G		intron	N/A	ENSP00000471242.1
	ENSG00000297447	ENST00000747954.1		n.50T>C		non_coding_transcript_exon	Exon 1 of 2

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

African (AFR) AF: 0.719 AC: 29806 AN: 41458

American (AMR) AF: 0.672 AC: 10276 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2055 AN: 3468

East Asian (EAS) AF: 0.709 AC: 3650 AN: 5146

South Asian (SAS) AF: 0.735 AC: 3549 AN: 4826

European-Finnish (FIN) AF: 0.716 AC: 7553 AN: 10548

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44700 AN: 67970

Other (OTH) AF: 0.672 AC: 1419 AN: 2112

Alfa AF: 0.664 Hom.: 114818

Bravo AF: 0.677

Asia WGS AF: 0.727 AC: 2528 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	0.30
DANN	Benign	0.16
PhyloP100		-1.2
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: rs688872; hg19: chr13-98966317;