rs1391769

Variant names:

• chr3-69524251-T-C
• rs1391769
• ENST00000459638.5:c.-129+17955A>G

Variant summary

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

The ENST00000497880.5(FRMD4B):​c.-129+16904A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,126 control chromosomes in the GnomAD database, including 6,369 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 0.28 (6369 hom., cov: 32)
• Consequence: FRMD4B ENST00000497880.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341
• Publications: 2 publications found

Genes affected

FRMD4B (HGNC:24886): (FERM domain containing 4B) This gene encodes a GRP1-binding protein which contains a FERM protein interaction domain as well as two coiled coil domains. This protein may play a role as a scaffolding protein. [provided by RefSeq, Mar 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000497880.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRMD4B	ENST00000459638.5	TSL:5	c.-129+17955A>G		intron	N/A	ENSP00000417550.1	C9JA15
	FRMD4B	ENST00000497880.5	TSL:4	c.-129+16904A>G		intron	N/A	ENSP00000417765.1	C9J7M5

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43295 AN: 152008 Hom.: 6370 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.285 AC: 43308 AN: 152126 Hom.: 6369 Cov.: 32 AF XY: 0.284 AC XY: 21104 AN XY: 74366

African (AFR) AF: 0.312 AC: 12960 AN: 41516

American (AMR) AF: 0.208 AC: 3174 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 712 AN: 3472

East Asian (EAS) AF: 0.112 AC: 581 AN: 5172

South Asian (SAS) AF: 0.190 AC: 914 AN: 4810

European-Finnish (FIN) AF: 0.343 AC: 3623 AN: 10572

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20465 AN: 67980

Other (OTH) AF: 0.266 AC: 563 AN: 2116

Alfa AF: 0.288 Hom.: 5192

Bravo AF: 0.274

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.81
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1391769; hg19: chr3-69573402;