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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0623 AC: 2588 AN: 41564

American (AMR) AF: 0.273 AC: 4164 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3468

East Asian (EAS) AF: 0.241 AC: 1241 AN: 5156

South Asian (SAS) AF: 0.301 AC: 1452 AN: 4820

European-Finnish (FIN) AF: 0.135 AC: 1434 AN: 10608

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9741 AN: 67988

Other (OTH) AF: 0.154 AC: 325 AN: 2114

Alfa AF: 0.149 Hom.: 1552

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1469259; hg19: chr4-117385666;