chr13-98230044-G-A

Variant names:

• chr13-98230044-G-A
• rs7989050
• NM_005766.4:c.171+16631G>A

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+16631G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,156 control chromosomes in the GnomAD database, including 4,563 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 0.16 (4563 hom., cov: 32)
• Consequence: FARP1 NM_005766.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FARP1	NM_005766.4	c.171+16631G>A		intron_variant	Intron 2 of 26	ENST00000319562.11	NP_005757.1
FARP1	NM_001286839.2	c.171+16631G>A		intron_variant	Intron 2 of 27		NP_001273768.1
FARP1	NM_001001715.4	c.172-14447G>A		intron_variant	Intron 2 of 2		NP_001001715.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FARP1	ENST00000319562.11	c.171+16631G>A		intron_variant	Intron 2 of 26	1	NM_005766.4	ENSP00000322926.6

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23786 AN: 152038 Hom.: 4540 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.0712

Gnomad FIN AF: 0.0371

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00873

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.157 AC: 23859 AN: 152156 Hom.: 4563 Cov.: 32 AF XY: 0.157 AC XY: 11651 AN XY: 74400

African (AFR) AF: 0.417 AC: 17293 AN: 41470

American (AMR) AF: 0.146 AC: 2238 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 161 AN: 3468

East Asian (EAS) AF: 0.488 AC: 2521 AN: 5168

South Asian (SAS) AF: 0.0716 AC: 345 AN: 4816

European-Finnish (FIN) AF: 0.0371 AC: 393 AN: 10604

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.00873 AC: 594 AN: 68014

Other (OTH) AF: 0.142 AC: 300 AN: 2114

Alfa AF: 0.0453 Hom.: 122

Bravo AF: 0.181

Asia WGS AF: 0.288 AC: 1001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.8
DANN	Benign	0.71
PhyloP100		0.072
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: rs7989050; hg19: chr13-98882298;