rs365302

chr6-159225301-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032532.3(FNDC1):c.885-234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,524 control chromosomes in the GnomAD database, including 14,139 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 0.38 (14139 hom., cov: 31)
• Consequence: FNDC1 NM_032532.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FNDC1	NM_032532.3	c.885-234T>C		intron_variant		ENST00000297267.14
FNDC1	XM_011536190.3	c.816-234T>C		intron_variant
FNDC1	XM_011536191.3	c.534-234T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FNDC1	ENST00000297267.14	c.885-234T>C		intron_variant		1	NM_032532.3	P1
FNDC1	ENST00000329629.8	c.760-234T>C		intron_variant		1
FNDC1	ENST00000480856.1	n.520-234T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57833 AN: 151408 Hom.: 14093 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.382 AC: 57938 AN: 151524 Hom.: 14139 Cov.: 31 AF XY: 0.385 AC XY: 28491 AN XY: 74008

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.338

Alfa AF: 0.265 Hom.: 2606

Bravo AF: 0.403

Asia WGS AF: 0.553 AC: 1919 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	7.1
Dann	Benign	0.78

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

Publications

LitVar

Other links and lift over

dbSNP: rs365302; hg19: chr6-159646333;