rs9647379

Variant names:

• chr3-172067378-G-C
• rs9647379
• NM_022763.4:c.-29+27607G>C

Your query was ambiguous. Multiple possible variants found:

• chr3-172067378-G-C
• chr3-172067378-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.-29+27607G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,002 control chromosomes in the GnomAD database, including 9,023 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 0.32 (9023 hom., cov: 31)
• Consequence: FNDC3B NM_022763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445
• Publications: 29 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FNDC3B	NM_022763.4	c.-29+27607G>C		intron_variant	Intron 1 of 25	ENST00000415807.7	NP_073600.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FNDC3B	ENST00000415807.7	c.-29+27607G>C		intron_variant	Intron 1 of 25	1	NM_022763.4	ENSP00000411242.2

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48326 AN: 151884 Hom.: 9019 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.318 AC: 48343 AN: 152002 Hom.: 9023 Cov.: 31 AF XY: 0.320 AC XY: 23753 AN XY: 74280

African (AFR) AF: 0.110 AC: 4545 AN: 41496

American (AMR) AF: 0.384 AC: 5862 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1478 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1382 AN: 5176

South Asian (SAS) AF: 0.266 AC: 1285 AN: 4826

European-Finnish (FIN) AF: 0.435 AC: 4582 AN: 10538

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28035 AN: 67932

Other (OTH) AF: 0.350 AC: 737 AN: 2108

Alfa AF: 0.255 Hom.: 691

Bravo AF: 0.309

Asia WGS AF: 0.268 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.0
DANN	Benign	0.51
PhyloP100		0.45
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs9647379; hg19: chr3-171785168;