rs1888747

chr9-83540636-C-G

Variant summary

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

The XM_017014588.2(FRMD3):c.24+19534G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,054 control chromosomes in the GnomAD database, including 46,421 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 (46421 hom., cov: 31)
• Consequence: FRMD3 XM_017014588.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

FRMD3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FRMD3	XM_017014588.2	c.24+19534G>C		intron_variant
FRMD3	XM_024447487.2	c.-142+34274G>C		intron_variant
FRMD3	XM_047423155.1	c.-142+44917G>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117791 AN: 151936 Hom.: 46349 Cov.: 31

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.776 AC: 117924 AN: 152054 Hom.: 46421 Cov.: 31 AF XY: 0.776 AC XY: 57660 AN XY: 74308

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.806

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.743

Alfa AF: 0.755 Hom.: 5431

Bravo AF: 0.777

Asia WGS AF: 0.790 AC: 2750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.34
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1888747; hg19: chr9-86155551;