rs872606

Variant names:

• chr13-98240417-A-C
• rs872606
• NM_005766.4:c.171+27004A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-98240417-A-C
• chr13-98240417-A-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.171+27004A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,744 control chromosomes in the GnomAD database, including 14,292 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 0.43 (14292 hom., cov: 30)
• Consequence: FARP1 NM_005766.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 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.171+27004A>C		intron	N/A	NP_005757.1
	FARP1	NM_001286839.2		c.171+27004A>C		intron	N/A	NP_001273768.1
	FARP1	NM_001001715.4		c.172-4074A>C		intron	N/A	NP_001001715.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FARP1	ENST00000319562.11	TSL:1 MANE Select	c.171+27004A>C		intron	N/A	ENSP00000322926.6
	FARP1	ENST00000595437.5	TSL:1	c.171+27004A>C		intron	N/A	ENSP00000471242.1
	FARP1	ENST00000627049.2	TSL:5	c.171+27004A>C		intron	N/A	ENSP00000486285.1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65410 AN: 151626 Hom.: 14284 Cov.: 30

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.431 AC: 65463 AN: 151744 Hom.: 14292 Cov.: 30 AF XY: 0.434 AC XY: 32188 AN XY: 74134

African (AFR) AF: 0.405 AC: 16734 AN: 41350

American (AMR) AF: 0.429 AC: 6543 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1902 AN: 3470

East Asian (EAS) AF: 0.627 AC: 3210 AN: 5120

South Asian (SAS) AF: 0.434 AC: 2083 AN: 4798

European-Finnish (FIN) AF: 0.464 AC: 4880 AN: 10518

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.422 AC: 28659 AN: 67910

Other (OTH) AF: 0.465 AC: 981 AN: 2108

Alfa AF: 0.430 Hom.: 24414

Bravo AF: 0.429

Asia WGS AF: 0.484 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.52
PhyloP100		0.22
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: rs872606; hg19: chr13-98892671;