9-83548779-C-G

Variant names:

• chr9-83548779-C-G
• rs11140156
• XM_017014588.2:c.24+11391G>C

Variant summary

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

The XM_017014588.2(FRMD3):​c.24+11391G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0634 in 152,034 control chromosomes in the GnomAD database, including 430 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 (430 hom., cov: 32)
• Consequence: FRMD3 XM_017014588.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 2 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0634 AC: 9635 AN: 151916 Hom.: 430 Cov.: 32

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0869

Gnomad FIN AF: 0.0498

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0847

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0634 AC: 9637 AN: 152034 Hom.: 430 Cov.: 32 AF XY: 0.0635 AC XY: 4716 AN XY: 74322

African (AFR) AF: 0.0171 AC: 710 AN: 41480

American (AMR) AF: 0.0650 AC: 992 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0594 AC: 206 AN: 3468

East Asian (EAS) AF: 0.109 AC: 564 AN: 5174

South Asian (SAS) AF: 0.0874 AC: 421 AN: 4818

European-Finnish (FIN) AF: 0.0498 AC: 527 AN: 10582

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0847 AC: 5753 AN: 67936

Other (OTH) AF: 0.0647 AC: 137 AN: 2116

Alfa AF: 0.0741 Hom.: 58

Bravo AF: 0.0614

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	1.3
DANN	Benign	0.88
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs11140156; hg19: chr9-86163694;