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. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000741219.1(ENSG00000253613):​n.137-6999C>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 ENST00000741219.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 10 publications found

Genes affected

ENSG00000253613 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741219.1. 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
	ENSG00000253613	ENST00000507269.3	TSL:5	n.212+314C>T		intron	N/A
	ENSG00000253613	ENST00000741219.1		n.137-6999C>T		intron	N/A
	ENSG00000253613	ENST00000741220.1		n.137-7660C>T		intron	N/A

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

African (AFR) AF: 0.971 AC: 40366 AN: 41564

American (AMR) AF: 0.900 AC: 13776 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.878 AC: 3045 AN: 3470

East Asian (EAS) AF: 0.617 AC: 3188 AN: 5166

South Asian (SAS) AF: 0.916 AC: 4415 AN: 4820

European-Finnish (FIN) AF: 0.867 AC: 9184 AN: 10598

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57865 AN: 68018

Other (OTH) AF: 0.888 AC: 1879 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.97
DANN	Benign	0.32
PhyloP100		-0.040

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: rs2416259;

hg19: chr5-110419742;