rs2416259

Variant names:

• chr5-111084044-G-A
• rs2416259
• ENST00000507269.3:n.212+314C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-111084044-G-A
• chr5-111084044-G-T

Variant summary

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

The ENST00000507269.3(ENSG00000253613):​n.212+314C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 152,256 control chromosomes in the GnomAD database, including 60,123 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 0.89 (60123 hom., cov: 33)
• Consequence: ENSG00000253613 ENST00000507269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

Genes affected

ENSG00000253613 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 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
ENSG00000253613	ENST00000507269.3	n.212+314C>T		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.885 AC: 134717 AN: 152138 Hom.: 60062 Cov.: 33

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.886 AC: 134836 AN: 152256 Hom.: 60123 Cov.: 33 AF XY: 0.884 AC XY: 65792 AN XY: 74452

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.888

Alfa AF: 0.875 Hom.: 8584

Bravo AF: 0.890

Asia WGS AF: 0.802 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.97
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2416259; hg19: chr5-110419742;