rs1535752

Variant names:

• chr9-83290338-G-A
• rs1535752
• NM_174938.6:c.1195+265C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-83290338-G-A
• chr9-83290338-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_174938.6(FRMD3):​c.1195+265C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,008 control chromosomes in the GnomAD database, including 24,400 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 0.55 (24400 hom., cov: 32)
• Consequence: FRMD3 NM_174938.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174938.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRMD3	NM_174938.6	MANE Select	c.1195+265C>T		intron	N/A	NP_777598.3
	FRMD3	NM_001244959.2		c.1195+265C>T		intron	N/A	NP_001231888.1	A2A2Y4-2
	FRMD3	NM_001244960.2		c.1063+265C>T		intron	N/A	NP_001231889.1	A2A2Y4-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRMD3	ENST00000304195.8	TSL:1 MANE Select	c.1195+265C>T		intron	N/A	ENSP00000303508.3	A2A2Y4-1
	FRMD3	ENST00000621208.4	TSL:1	c.1063+265C>T		intron	N/A	ENSP00000484839.1	A2A2Y4-5
	FRMD3	ENST00000376434.5	TSL:1	c.613+265C>T		intron	N/A	ENSP00000365617.1	A2A2Y4-3

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83295 AN: 151890 Hom.: 24383 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.548 AC: 83337 AN: 152008 Hom.: 24400 Cov.: 32 AF XY: 0.555 AC XY: 41253 AN XY: 74292

African (AFR) AF: 0.332 AC: 13764 AN: 41414

American (AMR) AF: 0.581 AC: 8872 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1955 AN: 3470

East Asian (EAS) AF: 0.688 AC: 3559 AN: 5172

South Asian (SAS) AF: 0.783 AC: 3767 AN: 4812

European-Finnish (FIN) AF: 0.690 AC: 7291 AN: 10574

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42036 AN: 67976

Other (OTH) AF: 0.584 AC: 1234 AN: 2112

Alfa AF: 0.575 Hom.: 4536

Bravo AF: 0.527

Asia WGS AF: 0.755 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.22
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1535752; hg19: chr9-85905253;