9-83550119-C-T

Variant names:

• chr9-83550119-C-T
• rs11535575
• XM_017014588.2:c.24+10051G>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+10051G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0627 in 151,956 control chromosomes in the GnomAD database, including 428 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 (428 hom., cov: 33)
• Consequence: FRMD3 XM_017014588.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0835 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: 0.0627 AC: 9523 AN: 151838 Hom.: 428 Cov.: 33

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.0595

Gnomad EAS AF: 0.0898

Gnomad SAS AF: 0.0853

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0627 AC: 9524 AN: 151956 Hom.: 428 Cov.: 33 AF XY: 0.0623 AC XY: 4630 AN XY: 74288

African (AFR) AF: 0.0172 AC: 712 AN: 41484

American (AMR) AF: 0.0650 AC: 992 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0595 AC: 206 AN: 3464

East Asian (EAS) AF: 0.0902 AC: 467 AN: 5176

South Asian (SAS) AF: 0.0855 AC: 412 AN: 4816

European-Finnish (FIN) AF: 0.0497 AC: 525 AN: 10564

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0846 AC: 5743 AN: 67874

Other (OTH) AF: 0.0649 AC: 137 AN: 2112

Alfa AF: 0.0573 Hom.: 160

Bravo AF: 0.0603

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.38
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs11535575; hg19: chr9-86165034;