rs9868872

Variant names:

• chr3-172211740-G-A
• rs9868872
• NM_022763.4:c.188-15131G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-172211740-G-A
• chr3-172211740-G-C
• chr3-172211740-G-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.188-15131G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 152,240 control chromosomes in the GnomAD database, including 60,533 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 (60533 hom., cov: 32)
• Consequence: FNDC3B NM_022763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FNDC3B	NM_022763.4	c.188-15131G>A		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.188-15131G>A		intron_variant	Intron 3 of 25	1	NM_022763.4	ENSP00000411242.2

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135362 AN: 152122 Hom.: 60498 Cov.: 32

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.890 AC: 135448 AN: 152240 Hom.: 60533 Cov.: 32 AF XY: 0.883 AC XY: 65730 AN XY: 74416

African (AFR) AF: 0.948 AC: 39382 AN: 41544

American (AMR) AF: 0.805 AC: 12324 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3198 AN: 3472

East Asian (EAS) AF: 0.670 AC: 3459 AN: 5166

South Asian (SAS) AF: 0.876 AC: 4229 AN: 4826

European-Finnish (FIN) AF: 0.836 AC: 8868 AN: 10602

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

European-Non Finnish (NFE) AF: 0.898 AC: 61057 AN: 68010

Other (OTH) AF: 0.895 AC: 1890 AN: 2112

Alfa AF: 0.865 Hom.: 3030

Bravo AF: 0.891

Asia WGS AF: 0.771 AC: 2682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.026
DANN	Benign	0.27
PhyloP100		-1.5
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: rs9868872; hg19: chr3-171929530;