3-69204505-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015123.3(FRMD4B):​c.877-5731A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0899 in 152,282 control chromosomes in the GnomAD database, including 633 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 0.090 ( 633 hom., cov: 32)

Consequence

FRMD4B
NM_015123.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.236
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FRMD4BNM_015123.3 linkuse as main transcriptc.877-5731A>G intron_variant ENST00000398540.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FRMD4BENST00000398540.8 linkuse as main transcriptc.877-5731A>G intron_variant 1 NM_015123.3 P1Q9Y2L6-1
FRMD4BENST00000470070.6 linkuse as main transcriptn.771-5731A>G intron_variant, non_coding_transcript_variant 5
FRMD4BENST00000483668.5 linkuse as main transcriptn.489-5731A>G intron_variant, non_coding_transcript_variant 4
FRMD4BENST00000487751.1 linkuse as main transcriptn.502-5731A>G intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.0899
AC:
13672
AN:
152164
Hom.:
632
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.105
Gnomad AMI
AF:
0.0769
Gnomad AMR
AF:
0.0728
Gnomad ASJ
AF:
0.0764
Gnomad EAS
AF:
0.0129
Gnomad SAS
AF:
0.0314
Gnomad FIN
AF:
0.0747
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.0974
Gnomad OTH
AF:
0.0913
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0899
AC:
13685
AN:
152282
Hom.:
633
Cov.:
32
AF XY:
0.0871
AC XY:
6489
AN XY:
74492
show subpopulations
Gnomad4 AFR
AF:
0.105
Gnomad4 AMR
AF:
0.0726
Gnomad4 ASJ
AF:
0.0764
Gnomad4 EAS
AF:
0.0129
Gnomad4 SAS
AF:
0.0315
Gnomad4 FIN
AF:
0.0747
Gnomad4 NFE
AF:
0.0974
Gnomad4 OTH
AF:
0.0903
Alfa
AF:
0.0928
Hom.:
69
Bravo
AF:
0.0911
Asia WGS
AF:
0.0270
AC:
95
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
5.1
DANN
Benign
0.49

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6776243; hg19: chr3-69253656; API