rs7470287

Variant names:

• chr9-83557750-G-C
• rs7470287
• XM_017014588.2:c.24+2420C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-83557750-G-C
• chr9-83557750-G-T

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+2420C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,990 control chromosomes in the GnomAD database, including 15,215 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 0.44 (15215 hom., cov: 32)
• Consequence: FRMD3 XM_017014588.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.469 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: 0.442 AC: 67059 AN: 151874 Hom.: 15192 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.442 AC: 67124 AN: 151990 Hom.: 15215 Cov.: 32 AF XY: 0.434 AC XY: 32235 AN XY: 74274

African (AFR) AF: 0.428 AC: 17748 AN: 41438

American (AMR) AF: 0.479 AC: 7308 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1717 AN: 3464

East Asian (EAS) AF: 0.222 AC: 1150 AN: 5178

South Asian (SAS) AF: 0.447 AC: 2154 AN: 4822

European-Finnish (FIN) AF: 0.315 AC: 3320 AN: 10530

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32008 AN: 67968

Other (OTH) AF: 0.472 AC: 998 AN: 2114

Alfa AF: 0.290 Hom.: 653

Bravo AF: 0.455

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.60
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs7470287; hg19: chr9-86172665;