chr9-83548779-C-G

Variant names:

• chr9-83548779-C-G
• rs11140156
• XM_017014588.2:c.24+11391G>C

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+11391G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0634 in 152,034 control chromosomes in the GnomAD database, including 430 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 0.063 (430 hom., cov: 32)
• Consequence: FRMD3 XM_017014588.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 2 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRMD3	XM_017014588.2	c.24+11391G>C		intron_variant	Intron 1 of 13		XP_016870077.1
FRMD3	XM_024447487.2	c.-142+26131G>C		intron_variant	Intron 2 of 14		XP_024303255.1
FRMD3	XM_047423155.1	c.-142+36774G>C		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: 0.0634 AC: 9635 AN: 151916 Hom.: 430 Cov.: 32

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0869

Gnomad FIN AF: 0.0498

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0847

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0634 AC: 9637 AN: 152034 Hom.: 430 Cov.: 32 AF XY: 0.0635 AC XY: 4716 AN XY: 74322

African (AFR) AF: 0.0171 AC: 710 AN: 41480

American (AMR) AF: 0.0650 AC: 992 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0594 AC: 206 AN: 3468

East Asian (EAS) AF: 0.109 AC: 564 AN: 5174

South Asian (SAS) AF: 0.0874 AC: 421 AN: 4818

European-Finnish (FIN) AF: 0.0498 AC: 527 AN: 10582

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0847 AC: 5753 AN: 67936

Other (OTH) AF: 0.0647 AC: 137 AN: 2116

Alfa AF: 0.0741 Hom.: 58

Bravo AF: 0.0614

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	1.3
DANN	Benign	0.88
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs11140156; hg19: chr9-86163694;