NM_032532.3:c.767-864C>A

Variant names:

• chr6-159222664-C-A
• rs2782552
• NM_032532.3:c.767-864C>A

Variant summary

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

The NM_032532.3(FNDC1):​c.767-864C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,066 control chromosomes in the GnomAD database, including 14,273 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 (14273 hom., cov: 33)
• Consequence: FNDC1 NM_032532.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FNDC1	NM_032532.3	c.767-864C>A		intron_variant	Intron 6 of 22	ENST00000297267.14	NP_115921.2
FNDC1	XM_011536190.3	c.698-864C>A		intron_variant	Intron 5 of 21		XP_011534492.1
FNDC1	XM_011536191.3	c.416-864C>A		intron_variant	Intron 3 of 19		XP_011534493.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FNDC1	ENST00000297267.14	c.767-864C>A		intron_variant	Intron 6 of 22	1	NM_032532.3	ENSP00000297267.9
FNDC1	ENST00000329629.8	c.641-864C>A		intron_variant	Intron 5 of 20	1		ENSP00000333297.8
FNDC1	ENST00000480856.1	n.402-864C>A		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58177 AN: 151948 Hom.: 14228 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.383 AC: 58282 AN: 152066 Hom.: 14273 Cov.: 33 AF XY: 0.386 AC XY: 28692 AN XY: 74338

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.340

Alfa AF: 0.314 Hom.: 1545

Bravo AF: 0.402

Asia WGS AF: 0.553 AC: 1920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.49

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: rs2782552; hg19: chr6-159643696;