rs17813699

Variant names:

• chr10-103922109-G-A
• rs17813699
• ENST00000698239.1:n.274-4453C>T

Variant summary

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

The ENST00000698239.1(ENSG00000289744):​n.274-4453C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.064 in 152,268 control chromosomes in the GnomAD database, including 446 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 0.064 (446 hom., cov: 32)
• Consequence: ENSG00000289744 ENST00000698239.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.982

Genes affected

ENSG00000289744 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.0949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289744	ENST00000698239.1	n.274-4453C>T		intron_variant	Intron 2 of 11
ENSG00000289744	ENST00000698240.1	n.389-4453C>T		intron_variant	Intron 2 of 10

Frequencies

GnomAD3 genomes AF: 0.0640 AC: 9744 AN: 152150 Hom.: 447 Cov.: 32

Gnomad AFR AF: 0.0155

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0384

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0192

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0640 AC: 9744 AN: 152268 Hom.: 446 Cov.: 32 AF XY: 0.0641 AC XY: 4769 AN XY: 74448

Gnomad4 AFR AF: 0.0154

Gnomad4 AMR AF: 0.0384

Gnomad4 ASJ AF: 0.0562

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0197

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.0968

Gnomad4 OTH AF: 0.0535

Alfa AF: 0.0844 Hom.: 351

Bravo AF: 0.0534

Asia WGS AF: 0.00664 AC: 24 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	0.13
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17813699; hg19: chr10-105681867;