9-83550119-C-T

Position:

• chr9-83550119-C-T

Variant summary

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

The XM_017014588.2(FRMD3):​c.24+10051G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0627 in 151,956 control chromosomes in the GnomAD database, including 428 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 0.063 (428 hom., cov: 33)
• Consequence: FRMD3 XM_017014588.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRMD3	XM_017014588.2	c.24+10051G>A		intron_variant			XP_016870077.1
FRMD3	XM_024447487.2	c.-142+24791G>A		intron_variant			XP_024303255.1
FRMD3	XM_047423155.1	c.-142+35434G>A		intron_variant			XP_047279111.1
		n.83550119C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0627 AC: 9523 AN: 151838 Hom.: 428 Cov.: 33

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.0595

Gnomad EAS AF: 0.0898

Gnomad SAS AF: 0.0853

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0627 AC: 9524 AN: 151956 Hom.: 428 Cov.: 33 AF XY: 0.0623 AC XY: 4630 AN XY: 74288

Gnomad4 AFR AF: 0.0172

Gnomad4 AMR AF: 0.0650

Gnomad4 ASJ AF: 0.0595

Gnomad4 EAS AF: 0.0902

Gnomad4 SAS AF: 0.0855

Gnomad4 FIN AF: 0.0497

Gnomad4 NFE AF: 0.0846

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0555 Hom.: 130

Bravo AF: 0.0603

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11535575; hg19: chr9-86165034;