rs1285082

Variant names:

• chr3-172395534-G-T
• rs1285082
• NM_022763.4:c.3304-1630G>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.3304-1630G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,940 control chromosomes in the GnomAD database, including 15,510 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 0.43 (15510 hom., cov: 32)
• Consequence: FNDC3B NM_022763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FNDC3B	NM_022763.4	c.3304-1630G>T		intron_variant	Intron 25 of 25	ENST00000415807.7	NP_073600.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FNDC3B	ENST00000415807.7	c.3304-1630G>T		intron_variant	Intron 25 of 25	1	NM_022763.4	ENSP00000411242.2
FNDC3B	ENST00000336824.8	c.3304-1630G>T		intron_variant	Intron 25 of 25	1		ENSP00000338523.4
FNDC3B	ENST00000416957.5	c.3304-1630G>T		intron_variant	Intron 25 of 25	1		ENSP00000389094.1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64557 AN: 151824 Hom.: 15514 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.425 AC: 64582 AN: 151940 Hom.: 15510 Cov.: 32 AF XY: 0.419 AC XY: 31101 AN XY: 74258

African (AFR) AF: 0.213 AC: 8813 AN: 41444

American (AMR) AF: 0.433 AC: 6600 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1611 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1063 AN: 5162

South Asian (SAS) AF: 0.365 AC: 1756 AN: 4810

European-Finnish (FIN) AF: 0.503 AC: 5299 AN: 10532

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.559 AC: 37968 AN: 67962

Other (OTH) AF: 0.406 AC: 854 AN: 2104

Alfa AF: 0.505 Hom.: 61337

Bravo AF: 0.411

Asia WGS AF: 0.290 AC: 1007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.57
PhyloP100		-0.87
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: rs1285082; hg19: chr3-172113324;