rs310612

Variant names:

• chr20-63550155-A-G
• rs310612
• ENST00000611891.1:c.-11+1716A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611891.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FNDC11	ENST00000611891.1	TSL:3	c.-11+1716A>G		intron	N/A	ENSP00000483577.1

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

African (AFR) AF: 0.850 AC: 35279 AN: 41486

American (AMR) AF: 0.242 AC: 3695 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3466

East Asian (EAS) AF: 0.233 AC: 1203 AN: 5158

South Asian (SAS) AF: 0.400 AC: 1927 AN: 4822

European-Finnish (FIN) AF: 0.148 AC: 1563 AN: 10584

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14209 AN: 67972

Other (OTH) AF: 0.360 AC: 760 AN: 2110

Alfa AF: 0.294 Hom.: 3204

Bravo AF: 0.417

Asia WGS AF: 0.436 AC: 1519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.26
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs310612; hg19: chr20-62181508;