rs294882

Variant names:

• chr6-159181969-T-C
• rs294882
• NM_032532.3:c.109+12264T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-159181969-T-C
• chr6-159181969-T-G

Variant summary

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

The NM_032532.3(FNDC1):​c.109+12264T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,946 control chromosomes in the GnomAD database, including 22,444 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 0.54 (22444 hom., cov: 31)
• Consequence: FNDC1 NM_032532.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327
• Publications: 6 publications found

Genes affected

FNDC1 (HGNC:21184): (fibronectin type III domain containing 1) Predicted to act upstream of or within several processes, including cellular response to hypoxia; positive regulation of cardiac muscle cell apoptotic process; and positive regulation of protein phosphorylation. Located in nuclear speck. [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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FNDC1	NM_032532.3	c.109+12264T>C		intron_variant	Intron 1 of 22	ENST00000297267.14	NP_115921.2
FNDC1	XM_011536190.3	c.109+12264T>C		intron_variant	Intron 1 of 21		XP_011534492.1
FNDC1	XM_011536191.3	c.109+12264T>C		intron_variant	Intron 1 of 19		XP_011534493.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FNDC1	ENST00000297267.14	c.109+12264T>C		intron_variant	Intron 1 of 22	1	NM_032532.3	ENSP00000297267.9

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81991 AN: 151828 Hom.: 22424 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.540 AC: 82045 AN: 151946 Hom.: 22444 Cov.: 31 AF XY: 0.537 AC XY: 39876 AN XY: 74272

African (AFR) AF: 0.597 AC: 24744 AN: 41424

American (AMR) AF: 0.441 AC: 6738 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1955 AN: 3466

East Asian (EAS) AF: 0.507 AC: 2618 AN: 5164

South Asian (SAS) AF: 0.494 AC: 2376 AN: 4814

European-Finnish (FIN) AF: 0.528 AC: 5560 AN: 10526

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.533 AC: 36248 AN: 67954

Other (OTH) AF: 0.543 AC: 1146 AN: 2110

Alfa AF: 0.538 Hom.: 8520

Bravo AF: 0.532

Asia WGS AF: 0.486 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.62
PhyloP100		0.33
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: rs294882; hg19: chr6-159603001;