rs1469259

Variant names:

• chr4-116464510-T-C
• rs1469259

Your query was ambiguous. Multiple possible variants found:

• chr4-116464510-T-C
• chr4-116464510-T-G

Variant summary

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

The variant allele was found at a frequency of 0.143 in 152,194 control chromosomes in the GnomAD database, including 1,971 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 0.14 (1971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21707 AN: 152076 Hom.: 1964 Cov.: 32

Gnomad AFR AF: 0.0623

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.143 AC: 21734 AN: 152194 Hom.: 1971 Cov.: 32 AF XY: 0.148 AC XY: 11047 AN XY: 74400

Gnomad4 AFR AF: 0.0623

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.154

Alfa AF: 0.150 Hom.: 1414

Bravo AF: 0.148

Asia WGS AF: 0.261 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1469259; hg19: chr4-117385666;