rs11140096

chr9-83451119-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_174938.6(FRMD3):c.148-61411T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,906 control chromosomes in the GnomAD database, including 14,181 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 0.43 (14181 hom., cov: 31)
• Consequence: FRMD3 NM_174938.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FRMD3	NM_174938.6	c.148-61411T>C		intron_variant		ENST00000304195.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FRMD3	ENST00000304195.8	c.148-61411T>C		intron_variant		1	NM_174938.6	P1
FRMD3	ENST00000621208.4	c.15+16499T>C		intron_variant		1
FRMD3	ENST00000376438.5	c.148-61411T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65125 AN: 151788 Hom.: 14149 Cov.: 31

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.429 AC: 65203 AN: 151906 Hom.: 14181 Cov.: 31 AF XY: 0.429 AC XY: 31811 AN XY: 74222

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.431

Alfa AF: 0.394 Hom.: 8667

Bravo AF: 0.435

Asia WGS AF: 0.378 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
Cadd	Benign	10
Dann	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs11140096; hg19: chr9-86066034;