rs10868025

chr9-83549261-A-Gchr9-83549261-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017014588.2(FRMD3):c.24+10909T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,046 control chromosomes in the GnomAD database, including 7,893 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 0.30 (7893 hom., cov: 32)
• Consequence: FRMD3 XM_017014588.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

Genes affected

FRMD3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FRMD3	XM_017014588.2	c.24+10909T>C		intron_variant
FRMD3	XM_024447487.2	c.-142+25649T>C		intron_variant
FRMD3	XM_047423155.1	c.-142+36292T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46226 AN: 151928 Hom.: 7890 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.304 AC: 46236 AN: 152046 Hom.: 7893 Cov.: 32 AF XY: 0.303 AC XY: 22540 AN XY: 74308

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.331

Alfa AF: 0.331 Hom.: 1182

Bravo AF: 0.302

Asia WGS AF: 0.320 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.7
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10868025; hg19: chr9-86164176;