9-83540477-T-C

Variant names:

• chr9-83540477-T-C
• rs1888746
• XM_017014588.2:c.24+19693A>G

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+19693A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 152,138 control chromosomes in the GnomAD database, including 46,409 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 (46409 hom., cov: 32)
• Consequence: FRMD3 XM_017014588.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• 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=-0.76).
• 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: 117824 AN: 152020 Hom.: 46339 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.775 AC: 117954 AN: 152138 Hom.: 46409 Cov.: 32 AF XY: 0.775 AC XY: 57681 AN XY: 74380

African (AFR) AF: 0.927 AC: 38523 AN: 41538

American (AMR) AF: 0.739 AC: 11295 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2202 AN: 3466

East Asian (EAS) AF: 0.740 AC: 3827 AN: 5174

South Asian (SAS) AF: 0.806 AC: 3883 AN: 4818

European-Finnish (FIN) AF: 0.734 AC: 7763 AN: 10572

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

European-Non Finnish (NFE) AF: 0.706 AC: 48005 AN: 67978

Other (OTH) AF: 0.743 AC: 1567 AN: 2110

Alfa AF: 0.721 Hom.: 146644

Bravo AF: 0.777

Asia WGS AF: 0.790 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.95
DANN	Benign	0.90
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1888746; hg19: chr9-86155392;