rs8481

Variant names:

• chr13-98453141-G-A
• rs8481
• NM_005766.4:c.*4824G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-98453141-G-A
• chr13-98453141-G-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.*4824G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 1,610,474 control chromosomes in the GnomAD database, including 62,742 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 0.26 (5217 hom., cov: 32)
  • Exomes 𝑓: 0.28 (57525 hom.)
• Consequence: FARP1 NM_005766.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 12 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FARP1	NM_005766.4	c.*4824G>A		3_prime_UTR_variant	Exon 27 of 27	ENST00000319562.11	NP_005757.1
STK24	NM_001032296.4	c.*32C>T		3_prime_UTR_variant	Exon 11 of 11	ENST00000539966.6	NP_001027467.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FARP1	ENST00000319562.11	c.*4824G>A		3_prime_UTR_variant	Exon 27 of 27	1	NM_005766.4	ENSP00000322926.6
STK24	ENST00000539966.6	c.*32C>T		3_prime_UTR_variant	Exon 11 of 11	1	NM_001032296.4	ENSP00000442539.2

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39265 AN: 151804 Hom.: 5206 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.258

GnomAD2 exomes AF: 0.252 AC: 62844 AN: 249726 AF XY: 0.253

Gnomad AFR exome AF: 0.228

Gnomad AMR exome AF: 0.217

Gnomad ASJ exome AF: 0.260

Gnomad EAS exome AF: 0.159

Gnomad FIN exome AF: 0.235

Gnomad NFE exome AF: 0.290

Gnomad OTH exome AF: 0.244

GnomAD4 exome AF: 0.277 AC: 404655 AN: 1458552 Hom.: 57525 Cov.: 31 AF XY: 0.277 AC XY: 200727 AN XY: 725750

African (AFR) AF: 0.224 AC: 7459 AN: 33358

American (AMR) AF: 0.218 AC: 9719 AN: 44544

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 6804 AN: 26110

East Asian (EAS) AF: 0.145 AC: 5747 AN: 39660

South Asian (SAS) AF: 0.230 AC: 19810 AN: 86078

European-Finnish (FIN) AF: 0.245 AC: 13023 AN: 53174

Middle Eastern (MID) AF: 0.217 AC: 1241 AN: 5720

European-Non Finnish (NFE) AF: 0.293 AC: 324973 AN: 1109652

Other (OTH) AF: 0.264 AC: 15879 AN: 60256

GnomAD4 genome AF: 0.259 AC: 39301 AN: 151922 Hom.: 5217 Cov.: 32 AF XY: 0.254 AC XY: 18856 AN XY: 74238

African (AFR) AF: 0.227 AC: 9419 AN: 41432

American (AMR) AF: 0.242 AC: 3699 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3468

East Asian (EAS) AF: 0.154 AC: 797 AN: 5170

South Asian (SAS) AF: 0.214 AC: 1027 AN: 4810

European-Finnish (FIN) AF: 0.226 AC: 2376 AN: 10536

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

European-Non Finnish (NFE) AF: 0.297 AC: 20193 AN: 67924

Other (OTH) AF: 0.257 AC: 541 AN: 2102

Alfa AF: 0.242 Hom.: 1251

Bravo AF: 0.256

Asia WGS AF: 0.192 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.58
PhyloP100		-0.094
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: rs8481; hg19: chr13-99105395; COSMIC: COSV60345833; COSMIC: COSV60345833;