chr13-98451916-C-T

Variant names:

• chr13-98451916-C-T
• rs3742134
• NM_005766.4:c.*3599C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005766.4(FARP1):​c.*3599C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,036 control chromosomes in the GnomAD database, including 3,637 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 0.21 (3635 hom., cov: 32)
  • Exomes 𝑓: 0.19 (2 hom.)
• Consequence: FARP1 NM_005766.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 5 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]

STK24 (HGNC:11403): (serine/threonine kinase 24) This gene encodes a serine/threonine protein kinase that functions upstream of mitogen-activated protein kinase (MAPK) signaling. The encoded protein is cleaved into two chains by caspases; the N-terminal fragment (MST3/N) translocates to the nucleus and promotes programmed cells death. There is a pseudogene for this gene on chromosome X. 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 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.*3599C>T		3_prime_UTR	Exon 27 of 27	NP_005757.1
	STK24	NM_001032296.4	MANE Select	c.*1257G>A		3_prime_UTR	Exon 11 of 11	NP_001027467.2
	FARP1	NM_001286839.2		c.*3599C>T		3_prime_UTR	Exon 28 of 28	NP_001273768.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FARP1	ENST00000319562.11	TSL:1 MANE Select	c.*3599C>T		3_prime_UTR	Exon 27 of 27	ENSP00000322926.6
	STK24	ENST00000539966.6	TSL:1 MANE Select	c.*1257G>A		3_prime_UTR	Exon 11 of 11	ENSP00000442539.2
	STK24	ENST00000397517.6	TSL:2	c.*1257G>A		3_prime_UTR	Exon 10 of 10	ENSP00000380651.3

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32601 AN: 151846 Hom.: 3629 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.214

GnomAD4 exome AF: 0.194 AC: 14 AN: 72 Hom.: 2 Cov.: 0 AF XY: 0.250 AC XY: 11 AN XY: 44

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.219 AC: 14 AN: 64

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.215 AC: 32628 AN: 151964 Hom.: 3635 Cov.: 32 AF XY: 0.211 AC XY: 15646 AN XY: 74290

African (AFR) AF: 0.242 AC: 10020 AN: 41386

American (AMR) AF: 0.183 AC: 2792 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3472

East Asian (EAS) AF: 0.142 AC: 737 AN: 5176

South Asian (SAS) AF: 0.212 AC: 1019 AN: 4816

European-Finnish (FIN) AF: 0.168 AC: 1778 AN: 10562

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14761 AN: 67964

Other (OTH) AF: 0.217 AC: 457 AN: 2104

Alfa AF: 0.213 Hom.: 5641

Bravo AF: 0.215

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.57
DANN	Benign	0.66
PhyloP100		-1.3
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: rs3742134; hg19: chr13-99104170;