rs12493901

Variant names:

• chr3-172204265-G-A
• rs12493901
• NM_022763.4:c.188-22606G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-172204265-G-A
• chr3-172204265-G-C

Variant summary

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

The NM_022763.4(FNDC3B):​c.188-22606G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,040 control chromosomes in the GnomAD database, including 12,649 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 0.37 (12649 hom., cov: 32)
• Consequence: FNDC3B NM_022763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 14 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022763.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FNDC3B	NM_022763.4	MANE Select	c.188-22606G>A		intron	N/A	NP_073600.3
	FNDC3B	NM_001135095.2		c.188-22606G>A		intron	N/A	NP_001128567.1	Q53EP0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FNDC3B	ENST00000415807.7	TSL:1 MANE Select	c.188-22606G>A		intron	N/A	ENSP00000411242.2	Q53EP0-1
	FNDC3B	ENST00000336824.8	TSL:1	c.188-22606G>A		intron	N/A	ENSP00000338523.4	Q53EP0-1
	FNDC3B	ENST00000416957.5	TSL:1	c.188-22606G>A		intron	N/A	ENSP00000389094.1	Q53EP0-1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56400 AN: 151922 Hom.: 12655 Cov.: 32

Gnomad AFR AF: 0.0996

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.371 AC: 56388 AN: 152040 Hom.: 12649 Cov.: 32 AF XY: 0.371 AC XY: 27567 AN XY: 74288

African (AFR) AF: 0.0993 AC: 4123 AN: 41510

American (AMR) AF: 0.448 AC: 6840 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1597 AN: 3468

East Asian (EAS) AF: 0.428 AC: 2211 AN: 5168

South Asian (SAS) AF: 0.445 AC: 2143 AN: 4814

European-Finnish (FIN) AF: 0.467 AC: 4932 AN: 10550

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33118 AN: 67956

Other (OTH) AF: 0.424 AC: 892 AN: 2104

Alfa AF: 0.398 Hom.: 11154

Bravo AF: 0.358

Asia WGS AF: 0.422 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.76
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: rs12493901; hg19: chr3-171922055;