rs1888747

Variant names:

• chr9-83540636-C-G
• rs1888747
• XM_017014588.2:c.24+19534G>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+19534G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,054 control chromosomes in the GnomAD database, including 46,421 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 0.78 (46421 hom., cov: 31)
• Consequence: FRMD3 XM_017014588.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 29 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 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: 0.775 AC: 117791 AN: 151936 Hom.: 46349 Cov.: 31

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.776 AC: 117924 AN: 152054 Hom.: 46421 Cov.: 31 AF XY: 0.776 AC XY: 57660 AN XY: 74308

African (AFR) AF: 0.928 AC: 38532 AN: 41510

American (AMR) AF: 0.739 AC: 11285 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2201 AN: 3464

East Asian (EAS) AF: 0.741 AC: 3830 AN: 5172

South Asian (SAS) AF: 0.806 AC: 3872 AN: 4804

European-Finnish (FIN) AF: 0.736 AC: 7764 AN: 10552

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47984 AN: 67970

Other (OTH) AF: 0.743 AC: 1567 AN: 2108

Alfa AF: 0.755 Hom.: 5431

Bravo AF: 0.777

Asia WGS AF: 0.790 AC: 2750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.34
DANN	Benign	0.76
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1888747; hg19: chr9-86155551;