rs1359168

Variant names:

• chr9-83299328-A-C
• rs1359168
• NM_174938.6:c.927-142T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-83299328-A-C
• chr9-83299328-A-T

Variant summary

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

The NM_174938.6(FRMD3):​c.927-142T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 582,874 control chromosomes in the GnomAD database, including 99,029 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 0.49 (20519 hom., cov: 33)
  • Exomes 𝑓: 0.60 (78510 hom.)
• Consequence: FRMD3 NM_174938.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRMD3	NM_174938.6	c.927-142T>G		intron_variant	Intron 10 of 13	ENST00000304195.8	NP_777598.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRMD3	ENST00000304195.8	c.927-142T>G		intron_variant	Intron 10 of 13	1	NM_174938.6	ENSP00000303508.3

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74002 AN: 152006 Hom.: 20510 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.535

GnomAD4 exome AF: 0.598 AC: 257552 AN: 430750 Hom.: 78510 AF XY: 0.602 AC XY: 136235 AN XY: 226416

African (AFR) AF: 0.199 AC: 2194 AN: 11046

American (AMR) AF: 0.588 AC: 7362 AN: 12522

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 7379 AN: 13390

East Asian (EAS) AF: 0.644 AC: 18473 AN: 28694

South Asian (SAS) AF: 0.647 AC: 24700 AN: 38162

European-Finnish (FIN) AF: 0.653 AC: 24557 AN: 37584

Middle Eastern (MID) AF: 0.606 AC: 2095 AN: 3458

European-Non Finnish (NFE) AF: 0.600 AC: 156556 AN: 260968

Other (OTH) AF: 0.571 AC: 14236 AN: 24926

GnomAD4 genome AF: 0.487 AC: 74031 AN: 152124 Hom.: 20519 Cov.: 33 AF XY: 0.491 AC XY: 36523 AN XY: 74348

African (AFR) AF: 0.196 AC: 8151 AN: 41502

American (AMR) AF: 0.535 AC: 8176 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1882 AN: 3468

East Asian (EAS) AF: 0.635 AC: 3286 AN: 5174

South Asian (SAS) AF: 0.628 AC: 3028 AN: 4822

European-Finnish (FIN) AF: 0.646 AC: 6832 AN: 10574

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.598 AC: 40669 AN: 67996

Other (OTH) AF: 0.541 AC: 1141 AN: 2110

Alfa AF: 0.562 Hom.: 79000

Bravo AF: 0.466

Asia WGS AF: 0.623 AC: 2164 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	0.15
DANN	Benign	0.43
PhyloP100		-0.64
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: rs1359168; hg19: chr9-85914243;