9-83553777-C-T

Variant names:

• chr9-83553777-C-T
• rs6559732
• XM_017014588.2:c.24+6393G>A

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+6393G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,100 control chromosomes in the GnomAD database, including 49,735 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 0.81 (49735 hom., cov: 32)
• Consequence: FRMD3 XM_017014588.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122411 AN: 151982 Hom.: 49687 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.805 AC: 122512 AN: 152100 Hom.: 49735 Cov.: 32 AF XY: 0.802 AC XY: 59662 AN XY: 74350

African (AFR) AF: 0.723 AC: 29987 AN: 41472

American (AMR) AF: 0.864 AC: 13195 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2855 AN: 3470

East Asian (EAS) AF: 0.776 AC: 4011 AN: 5166

South Asian (SAS) AF: 0.825 AC: 3984 AN: 4830

European-Finnish (FIN) AF: 0.729 AC: 7701 AN: 10568

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58008 AN: 67996

Other (OTH) AF: 0.802 AC: 1695 AN: 2114

Alfa AF: 0.844 Hom.: 82880

Bravo AF: 0.811

Asia WGS AF: 0.796 AC: 2769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.0
DANN	Benign	0.40
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6559732; hg19: chr9-86168692;