chr9-83564648-T-C

Variant names:

• chr9-83564648-T-C
• rs4451390
• XM_024447487.2:c.-142+10262A>G

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+10262A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,206 control chromosomes in the GnomAD database, including 49,828 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 0.80 (49828 hom., cov: 33)
• Consequence: FRMD3 XM_024447487.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 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: 0.803 AC: 122197 AN: 152088 Hom.: 49756 Cov.: 33

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.804 AC: 122328 AN: 152206 Hom.: 49828 Cov.: 33 AF XY: 0.797 AC XY: 59339 AN XY: 74414

African (AFR) AF: 0.944 AC: 39211 AN: 41542

American (AMR) AF: 0.747 AC: 11414 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2530 AN: 3470

East Asian (EAS) AF: 0.621 AC: 3215 AN: 5176

South Asian (SAS) AF: 0.789 AC: 3810 AN: 4828

European-Finnish (FIN) AF: 0.679 AC: 7183 AN: 10574

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52295 AN: 68014

Other (OTH) AF: 0.793 AC: 1678 AN: 2116

Alfa AF: 0.777 Hom.: 206529

Bravo AF: 0.812

Asia WGS AF: 0.752 AC: 2615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.81
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4451390; hg19: chr9-86179563;