3-172344640-A-G

Position:

• chr3-172344640-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022763.4(FNDC3B):​c.2250+382A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,098 control chromosomes in the GnomAD database, including 17,305 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 0.45 (17305 hom., cov: 32)
• Consequence: FNDC3B NM_022763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FNDC3B	NM_022763.4	c.2250+382A>G		intron_variant		ENST00000415807.7	NP_073600.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FNDC3B	ENST00000415807.7	c.2250+382A>G		intron_variant		1	NM_022763.4	ENSP00000411242.2
FNDC3B	ENST00000336824.8	c.2250+382A>G		intron_variant		1		ENSP00000338523.4
FNDC3B	ENST00000416957.5	c.2250+382A>G		intron_variant		1		ENSP00000389094.1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67794 AN: 151980 Hom.: 17301 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.446 AC: 67814 AN: 152098 Hom.: 17305 Cov.: 32 AF XY: 0.440 AC XY: 32710 AN XY: 74334

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.410

Alfa AF: 0.541 Hom.: 10286

Bravo AF: 0.427

Asia WGS AF: 0.347 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.78

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

Other links and lift over

dbSNP: rs601277; hg19: chr3-172062430;