6-159222664-C-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032532.3. 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
	FNDC1	NM_032532.3	MANE Select	c.767-864C>A		intron	N/A	NP_115921.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FNDC1	ENST00000297267.14	TSL:1 MANE Select	c.767-864C>A		intron	N/A	ENSP00000297267.9
	FNDC1	ENST00000329629.8	TSL:1	c.641-864C>A		intron	N/A	ENSP00000333297.8
	FNDC1	ENST00000480856.1	TSL:3	n.402-864C>A		intron	N/A

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

African (AFR) AF: 0.666 AC: 27610 AN: 41462

American (AMR) AF: 0.302 AC: 4621 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3470

East Asian (EAS) AF: 0.730 AC: 3773 AN: 5168

South Asian (SAS) AF: 0.404 AC: 1946 AN: 4818

European-Finnish (FIN) AF: 0.246 AC: 2605 AN: 10576

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15984 AN: 67974

Other (OTH) AF: 0.340 AC: 719 AN: 2112

Alfa AF: 0.324 Hom.: 1712

Bravo AF: 0.402

Asia WGS AF: 0.553 AC: 1920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.49
PhyloP100		-0.38
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: rs2782552; hg19: chr6-159643696;