3-172203779-C-T

Variant names:

• chr3-172203779-C-T
• rs9854411
• NM_022763.4:c.188-23092C>T

Variant summary

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

The NM_022763.4(FNDC3B):​c.188-23092C>T 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 152,184 control chromosomes in the GnomAD database, including 60,790 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 (60790 hom., cov: 31)
• Consequence: FNDC3B NM_022763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 3 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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 rank	MANE	Protein	UniProt
FNDC3B	NM_022763.4	c.188-23092C>T		intron_variant	Intron 3 of 25	ENST00000415807.7	NP_073600.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FNDC3B	ENST00000415807.7	c.188-23092C>T		intron_variant	Intron 3 of 25	1	NM_022763.4	ENSP00000411242.2

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135612 AN: 152066 Hom.: 60755 Cov.: 31

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.892 AC: 135699 AN: 152184 Hom.: 60790 Cov.: 31 AF XY: 0.885 AC XY: 65855 AN XY: 74404

African (AFR) AF: 0.950 AC: 39444 AN: 41534

American (AMR) AF: 0.807 AC: 12325 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3241 AN: 3472

East Asian (EAS) AF: 0.670 AC: 3469 AN: 5176

South Asian (SAS) AF: 0.876 AC: 4219 AN: 4816

European-Finnish (FIN) AF: 0.837 AC: 8867 AN: 10594

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61202 AN: 68010

Other (OTH) AF: 0.896 AC: 1893 AN: 2112

Alfa AF: 0.895 Hom.: 7896

Bravo AF: 0.892

Asia WGS AF: 0.775 AC: 2696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.36
PhyloP100		-0.013
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: rs9854411; hg19: chr3-171921569;