XM_024447487.2:c.-142+12424C>T

Variant names:

• chr9-83562486-G-A
• rs3934902
• XM_024447487.2:c.-142+12424C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_024447487.2(FRMD3):​c.-142+12424C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,052 control chromosomes in the GnomAD database, including 2,687 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 0.18 (2687 hom., cov: 32)
• Consequence: FRMD3 XM_024447487.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRMD3	XM_024447487.2	c.-142+12424C>T		intron_variant	Intron 2 of 14		XP_024303255.1
FRMD3	XM_047423155.1	c.-142+23067C>T		intron_variant	Intron 1 of 13		XP_047279111.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27635 AN: 151934 Hom.: 2685 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.182 AC: 27653 AN: 152052 Hom.: 2687 Cov.: 32 AF XY: 0.185 AC XY: 13778 AN XY: 74320

African (AFR) AF: 0.138 AC: 5739 AN: 41482

American (AMR) AF: 0.175 AC: 2677 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 435 AN: 3466

East Asian (EAS) AF: 0.355 AC: 1831 AN: 5164

South Asian (SAS) AF: 0.256 AC: 1233 AN: 4808

European-Finnish (FIN) AF: 0.202 AC: 2135 AN: 10556

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13098 AN: 67980

Other (OTH) AF: 0.166 AC: 350 AN: 2110

Alfa AF: 0.188 Hom.: 8976

Bravo AF: 0.175

Asia WGS AF: 0.271 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.70
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs3934902; hg19: chr9-86177401;