rs6803181

Variant names:

• chr3-172214466-C-T
• rs6803181
• NM_022763.4:c.188-12405C>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.188-12405C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,122 control chromosomes in the GnomAD database, including 54,207 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 0.84 (54207 hom., cov: 31)
• Consequence: FNDC3B NM_022763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 4 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=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FNDC3B	NM_022763.4	c.188-12405C>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.188-12405C>T		intron_variant	Intron 3 of 25	1	NM_022763.4	ENSP00000411242.2

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127963 AN: 152004 Hom.: 54189 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.842 AC: 128029 AN: 152122 Hom.: 54207 Cov.: 31 AF XY: 0.837 AC XY: 62210 AN XY: 74350

African (AFR) AF: 0.776 AC: 32197 AN: 41476

American (AMR) AF: 0.790 AC: 12073 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3217 AN: 3472

East Asian (EAS) AF: 0.672 AC: 3474 AN: 5172

South Asian (SAS) AF: 0.875 AC: 4225 AN: 4828

European-Finnish (FIN) AF: 0.836 AC: 8828 AN: 10556

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61157 AN: 68020

Other (OTH) AF: 0.860 AC: 1820 AN: 2116

Alfa AF: 0.884 Hom.: 30431

Bravo AF: 0.835

Asia WGS AF: 0.759 AC: 2641 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.9
DANN	Benign	0.79
PhyloP100		-0.52
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: rs6803181; hg19: chr3-171932256;