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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRMD3	XM_017014588.2	c.24+2420C>G		intron_variant	Intron 1 of 13		XP_016870077.1
FRMD3	XM_024447487.2	c.-142+17160C>G		intron_variant	Intron 2 of 14		XP_024303255.1
FRMD3	XM_047423155.1	c.-142+27803C>G		intron_variant	Intron 1 of 13		XP_047279111.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;