rs6780871

Variant summary

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

The NM_022763.4(FNDC3B):​c.188-12055G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 152,290 control chromosomes in the GnomAD database, including 60,823 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 0.89 ( 60823 hom., cov: 34)

Consequence

FNDC3B
NM_022763.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44
Variant links:
Genes affected
FNDC3B (HGNC:24670): (fibronectin type III domain containing 3B) Enables RNA binding activity. Predicted to act upstream of or within several processes, including negative regulation of osteoblast differentiation; substrate adhesion-dependent cell spreading; and type II pneumocyte differentiation. Predicted to be located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

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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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FNDC3BNM_022763.4 linkuse as main transcriptc.188-12055G>A intron_variant ENST00000415807.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FNDC3BENST00000415807.7 linkuse as main transcriptc.188-12055G>A intron_variant 1 NM_022763.4 P1Q53EP0-1

Frequencies

GnomAD3 genomes
AF:
0.892
AC:
135695
AN:
152172
Hom.:
60788
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.950
Gnomad AMI
AF:
0.843
Gnomad AMR
AF:
0.808
Gnomad ASJ
AF:
0.933
Gnomad EAS
AF:
0.671
Gnomad SAS
AF:
0.876
Gnomad FIN
AF:
0.836
Gnomad MID
AF:
0.937
Gnomad NFE
AF:
0.900
Gnomad OTH
AF:
0.900
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.892
AC:
135782
AN:
152290
Hom.:
60823
Cov.:
34
AF XY:
0.885
AC XY:
65892
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.950
Gnomad4 AMR
AF:
0.807
Gnomad4 ASJ
AF:
0.933
Gnomad4 EAS
AF:
0.671
Gnomad4 SAS
AF:
0.876
Gnomad4 FIN
AF:
0.836
Gnomad4 NFE
AF:
0.900
Gnomad4 OTH
AF:
0.897
Alfa
AF:
0.893
Hom.:
7551
Bravo
AF:
0.892
Asia WGS
AF:
0.771
AC:
2684
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.043
DANN
Benign
0.41

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: rs6780871; hg19: chr3-171932606; API