rs2416259

Positions:

• chr5-111084044-G-A

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, non coding transcript 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: ENST00000507269.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000507269.3	n.212+314C>T		intron_variant, non_coding_transcript_variant		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;