rs11140096

Variant names:

• chr9-83451119-A-G
• rs11140096
• NM_174938.6:c.148-61411T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_174938.6(FRMD3):​c.148-61411T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,906 control chromosomes in the GnomAD database, including 14,181 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 0.43 (14181 hom., cov: 31)
• Consequence: FRMD3 NM_174938.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRMD3	NM_174938.6	c.148-61411T>C		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.148-61411T>C		intron_variant	Intron 1 of 13	1	NM_174938.6	ENSP00000303508.3
FRMD3	ENST00000621208.4	c.15+16499T>C		intron_variant	Intron 1 of 13	1		ENSP00000484839.1
FRMD3	ENST00000376438.5	c.148-61411T>C		intron_variant	Intron 1 of 14	2		ENSP00000365621.1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65125 AN: 151788 Hom.: 14149 Cov.: 31

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.429 AC: 65203 AN: 151906 Hom.: 14181 Cov.: 31 AF XY: 0.429 AC XY: 31811 AN XY: 74222

African (AFR) AF: 0.519 AC: 21474 AN: 41408

American (AMR) AF: 0.425 AC: 6477 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1308 AN: 3472

East Asian (EAS) AF: 0.431 AC: 2229 AN: 5170

South Asian (SAS) AF: 0.395 AC: 1896 AN: 4804

European-Finnish (FIN) AF: 0.433 AC: 4562 AN: 10540

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25850 AN: 67956

Other (OTH) AF: 0.431 AC: 907 AN: 2106

Alfa AF: 0.395 Hom.: 10213

Bravo AF: 0.435

Asia WGS AF: 0.378 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	10
DANN	Benign	0.80
PhyloP100		0.73
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: rs11140096; hg19: chr9-86066034;