rs13289150

Positions:

• chr9-83549513-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017014588.2(FRMD3):​c.24+10657T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,018 control chromosomes in the GnomAD database, including 7,891 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 0.30 (7891 hom., cov: 32)
• Consequence: FRMD3 XM_017014588.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

Genes affected

FRMD3 (HGNC:24125): (FERM domain containing 3) The protein encoded by this gene is a single pass membrane protein primarily found in ovaries. A similar protein in erythrocytes helps determine the shape of red blood cells, but the function of the encoded protein has not been determined. There is some evidence that this is a tumor suppressor gene, and there is also evidence linking defects in this gene to susceptibility to diabetic nephropathy in type 1 diabetes. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRMD3	XM_017014588.2	c.24+10657T>C		intron_variant			XP_016870077.1
FRMD3	XM_024447487.2	c.-142+25397T>C		intron_variant			XP_024303255.1
FRMD3	XM_047423155.1	c.-142+36040T>C		intron_variant			XP_047279111.1
		n.83549513A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46221 AN: 151900 Hom.: 7888 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.304 AC: 46231 AN: 152018 Hom.: 7891 Cov.: 32 AF XY: 0.303 AC XY: 22531 AN XY: 74288

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.330

Alfa AF: 0.358 Hom.: 10320

Bravo AF: 0.302

Asia WGS AF: 0.320 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13289150; hg19: chr9-86164428;