rs4097644

chr9-83495365-G-A

Variant summary

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

The NM_174938.6(FRMD3):c.147+42720C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,982 control chromosomes in the GnomAD database, including 19,436 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 0.50 (19436 hom., cov: 32)
• Consequence: FRMD3 NM_174938.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FRMD3	NM_174938.6	c.147+42720C>T		intron_variant		ENST00000304195.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FRMD3	ENST00000304195.8	c.147+42720C>T		intron_variant		1	NM_174938.6	P1
FRMD3	ENST00000376438.5	c.147+42720C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75772 AN: 151864 Hom.: 19424 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.0859

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.499 AC: 75822 AN: 151982 Hom.: 19436 Cov.: 32 AF XY: 0.494 AC XY: 36715 AN XY: 74264

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.0857

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.523

Alfa AF: 0.508 Hom.: 9995

Bravo AF: 0.504

Asia WGS AF: 0.331 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.3
Dann	Benign	0.82
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs4097644; hg19: chr9-86110280;