rs310612

chr20-63550155-A-G

Variant summary

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

The ENST00000611891.1(FNDC11):c.-11+1716A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,090 control chromosomes in the GnomAD database, including 18,076 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 0.39 (18076 hom., cov: 32)
• Consequence: FNDC11 ENST00000611891.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18

Genes affected

FNDC11 (HGNC:28764): (fibronectin type III domain containing 11)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FNDC11	ENST00000611891.1	c.-11+1716A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59505 AN: 151972 Hom.: 18007 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.392 AC: 59635 AN: 152090 Hom.: 18076 Cov.: 32 AF XY: 0.384 AC XY: 28542 AN XY: 74332

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.360

Alfa AF: 0.286 Hom.: 1595

Bravo AF: 0.417

Asia WGS AF: 0.436 AC: 1519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.7
Dann	Benign	0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs310612; hg19: chr20-62181508;