rs7614432

Variant names:

• chr3-172238631-T-C
• rs7614432
• NM_022763.4:c.265-8902T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-172238631-T-C
• chr3-172238631-T-G

Variant summary

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

The NM_022763.4(FNDC3B):​c.265-8902T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,160 control chromosomes in the GnomAD database, including 1,963 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 0.15 (1963 hom., cov: 32)
• Consequence: FNDC3B NM_022763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.224 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.265-8902T>C		intron	N/A	NP_073600.3
	FNDC3B	NM_001135095.2		c.265-8902T>C		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.265-8902T>C		intron	N/A	ENSP00000411242.2
	FNDC3B	ENST00000336824.8	TSL:1	c.265-8902T>C		intron	N/A	ENSP00000338523.4
	FNDC3B	ENST00000416957.5	TSL:1	c.265-8902T>C		intron	N/A	ENSP00000389094.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23248 AN: 152042 Hom.: 1963 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.153 AC: 23257 AN: 152160 Hom.: 1963 Cov.: 32 AF XY: 0.152 AC XY: 11276 AN XY: 74388

African (AFR) AF: 0.227 AC: 9437 AN: 41492

American (AMR) AF: 0.109 AC: 1671 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 715 AN: 3470

East Asian (EAS) AF: 0.137 AC: 709 AN: 5182

South Asian (SAS) AF: 0.209 AC: 1005 AN: 4812

European-Finnish (FIN) AF: 0.0948 AC: 1005 AN: 10602

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8191 AN: 67990

Other (OTH) AF: 0.147 AC: 310 AN: 2116

Alfa AF: 0.131 Hom.: 1968

Bravo AF: 0.156

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.46
DANN	Benign	0.48
PhyloP100		-1.1
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: rs7614432; hg19: chr3-171956421;