3-172215782-A-T

Variant names:

• chr3-172215782-A-T
• rs7619745
• NM_022763.4:c.188-11089A>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.188-11089A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,222 control chromosomes in the GnomAD database, including 59,228 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 0.88 (59228 hom., cov: 32)
• Consequence: FNDC3B NM_022763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.698
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FNDC3B	NM_022763.4	MANE Select	c.188-11089A>T		intron	N/A	NP_073600.3
	FNDC3B	NM_001135095.2		c.188-11089A>T		intron	N/A	NP_001128567.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FNDC3B	ENST00000415807.7	TSL:1 MANE Select	c.188-11089A>T		intron	N/A	ENSP00000411242.2
	FNDC3B	ENST00000336824.8	TSL:1	c.188-11089A>T		intron	N/A	ENSP00000338523.4
	FNDC3B	ENST00000416957.5	TSL:1	c.188-11089A>T		intron	N/A	ENSP00000389094.1

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133923 AN: 152104 Hom.: 59195 Cov.: 32

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.880 AC: 134008 AN: 152222 Hom.: 59228 Cov.: 32 AF XY: 0.874 AC XY: 65082 AN XY: 74422

African (AFR) AF: 0.932 AC: 38719 AN: 41544

American (AMR) AF: 0.798 AC: 12186 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 3195 AN: 3472

East Asian (EAS) AF: 0.675 AC: 3497 AN: 5182

South Asian (SAS) AF: 0.868 AC: 4189 AN: 4828

European-Finnish (FIN) AF: 0.832 AC: 8801 AN: 10584

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

European-Non Finnish (NFE) AF: 0.890 AC: 60509 AN: 68014

Other (OTH) AF: 0.886 AC: 1875 AN: 2116

Alfa AF: 0.850 Hom.: 2657

Bravo AF: 0.880

Asia WGS AF: 0.768 AC: 2673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.84
PhyloP100		0.70
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: rs7619745; hg19: chr3-171933572;