rs17709714

Variant names:

• chr14-85507411-A-C
• rs17709714
• ENST00000557547.1:n.110+9414T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000557547.1(ENSG00000258902):​n.110+9414T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,106 control chromosomes in the GnomAD database, including 2,886 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 0.18 (2886 hom., cov: 32)
• Consequence: ENSG00000258902 ENST00000557547.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18
• Publications: 3 publications found

Genes affected

ENSG00000258902 (HGNC:):

FLRT2-AS1 (HGNC:55912): (FLRT2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557547.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258902	ENST00000557547.1	TSL:4	n.110+9414T>G		intron	N/A
	ENSG00000258902	ENST00000790475.1		n.99+9414T>G		intron	N/A
	FLRT2-AS1	ENST00000790578.1		n.1479-13158T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26974 AN: 151988 Hom.: 2887 Cov.: 32

Gnomad AFR AF: 0.0885

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.177 AC: 26961 AN: 152106 Hom.: 2886 Cov.: 32 AF XY: 0.172 AC XY: 12796 AN XY: 74354

African (AFR) AF: 0.0883 AC: 3663 AN: 41498

American (AMR) AF: 0.193 AC: 2945 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3468

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5178

South Asian (SAS) AF: 0.0860 AC: 415 AN: 4824

European-Finnish (FIN) AF: 0.198 AC: 2098 AN: 10572

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16042 AN: 67976

Other (OTH) AF: 0.217 AC: 456 AN: 2106

Alfa AF: 0.195 Hom.: 570

Bravo AF: 0.177

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.7
DANN	Benign	0.64
PhyloP100		2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17709714;

hg19: chr14-85973755;