rs11793821

Positions:

• chr9-83569589-A-G

Variant summary

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

The XM_024447487.2(FRMD3):​c.-142+5321T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,108 control chromosomes in the GnomAD database, including 3,743 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 0.20 (3743 hom., cov: 32)
• Consequence: FRMD3 XM_024447487.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387

Genes affected

FRMD3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FRMD3	XM_024447487.2	c.-142+5321T>C		intron_variant
FRMD3	XM_047423155.1	c.-142+15964T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30097 AN: 151990 Hom.: 3727 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.198 AC: 30151 AN: 152108 Hom.: 3743 Cov.: 32 AF XY: 0.193 AC XY: 14378 AN XY: 74374

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0789

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.195

Alfa AF: 0.159 Hom.: 2135

Bravo AF: 0.211

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.4
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11793821; hg19: chr9-86184504;