rs2282048

chr13-98244898-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.171+31485A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 1,412,636 control chromosomes in the GnomAD database, including 108,510 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 0.32 (9516 hom., cov: 32)
  • Exomes 𝑓: 0.39 (98994 hom.)
• Consequence: FARP1 NM_005766.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FARP1	NM_005766.4	c.171+31485A>G		intron_variant		ENST00000319562.11
FARP1	NM_001001715.4	c.*189A>G		3_prime_UTR_variant	3/3
FARP1	NM_001286839.2	c.171+31485A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FARP1	ENST00000319562.11	c.171+31485A>G		intron_variant		1	NM_005766.4	P1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49147 AN: 151970 Hom.: 9523 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.378

GnomAD4 exome AF: 0.390 AC: 491862 AN: 1260548 Hom.: 98994 Cov.: 32 AF XY: 0.392 AC XY: 239514 AN XY: 610456

Gnomad4 AFR exome AF: 0.0959

Gnomad4 AMR exome AF: 0.369

Gnomad4 ASJ exome AF: 0.465

Gnomad4 EAS exome AF: 0.650

Gnomad4 SAS exome AF: 0.409

Gnomad4 FIN exome AF: 0.427

Gnomad4 NFE exome AF: 0.386

Gnomad4 OTH exome AF: 0.396

GnomAD4 genome AF: 0.323 AC: 49153 AN: 152088 Hom.: 9516 Cov.: 32 AF XY: 0.329 AC XY: 24431 AN XY: 74340

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.380

Alfa AF: 0.381 Hom.: 11485

Bravo AF: 0.312

Asia WGS AF: 0.452 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.18
Dann	Benign	0.21

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: rs2282048; hg19: chr13-98897152;