rs11793821

Variant names:

• chr9-83569589-A-G
• rs11793821
• XM_024447487.2:c.-142+5321T>C

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+5321T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,108 control chromosomes in the GnomAD database, including 3,743 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 0.20 (3743 hom., cov: 32)
• Consequence: FRMD3 XM_024447487.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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: 0.198 AC: 30097 AN: 151990 Hom.: 3727 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.198 AC: 30151 AN: 152108 Hom.: 3743 Cov.: 32 AF XY: 0.193 AC XY: 14378 AN XY: 74374

African (AFR) AF: 0.359 AC: 14875 AN: 41454

American (AMR) AF: 0.153 AC: 2342 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3468

East Asian (EAS) AF: 0.115 AC: 595 AN: 5164

South Asian (SAS) AF: 0.0789 AC: 381 AN: 4828

European-Finnish (FIN) AF: 0.100 AC: 1061 AN: 10592

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9832 AN: 67996

Other (OTH) AF: 0.195 AC: 412 AN: 2112

Alfa AF: 0.162 Hom.: 2690

Bravo AF: 0.211

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.4
DANN	Benign	0.86
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs11793821; hg19: chr9-86184504;