rs7863524

Variant names:

• chr9-83497819-G-T
• rs7863524
• NM_174938.6:c.147+40266C>A

Variant summary

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

The NM_174938.6(FRMD3):​c.147+40266C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,074 control chromosomes in the GnomAD database, including 32,659 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 0.65 (32659 hom., cov: 33)
• Consequence: FRMD3 NM_174938.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 4 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRMD3	NM_174938.6	c.147+40266C>A		intron_variant	Intron 1 of 13	ENST00000304195.8	NP_777598.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRMD3	ENST00000304195.8	c.147+40266C>A		intron_variant	Intron 1 of 13	1	NM_174938.6	ENSP00000303508.3
FRMD3	ENST00000376438.5	c.147+40266C>A		intron_variant	Intron 1 of 14	2		ENSP00000365621.1

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99069 AN: 151956 Hom.: 32616 Cov.: 33

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.652 AC: 99164 AN: 152074 Hom.: 32659 Cov.: 33 AF XY: 0.650 AC XY: 48355 AN XY: 74340

African (AFR) AF: 0.731 AC: 30300 AN: 41464

American (AMR) AF: 0.628 AC: 9594 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2429 AN: 3468

East Asian (EAS) AF: 0.417 AC: 2158 AN: 5172

South Asian (SAS) AF: 0.596 AC: 2872 AN: 4820

European-Finnish (FIN) AF: 0.642 AC: 6793 AN: 10576

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42766 AN: 67972

Other (OTH) AF: 0.672 AC: 1420 AN: 2114

Alfa AF: 0.631 Hom.: 134846

Bravo AF: 0.656

Asia WGS AF: 0.582 AC: 2027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.70
PhyloP100		0.0050
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: rs7863524; hg19: chr9-86112734;