rs1466462

Variant names:

• chr11-65651893-G-C
• rs1466462

Your query was ambiguous. Multiple possible variants found:

• chr11-65651893-G-C
• chr11-65651893-G-T

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 0.338 in 152,234 control chromosomes in the GnomAD database, including 9,238 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 0.34 (9238 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 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: 0.338 AC: 51388 AN: 152116 Hom.: 9233 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.338 AC: 51425 AN: 152234 Hom.: 9238 Cov.: 33 AF XY: 0.343 AC XY: 25541 AN XY: 74416

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.325

Alfa AF: 0.276 Hom.: 793

Bravo AF: 0.309

Asia WGS AF: 0.258 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1466462; hg19: chr11-65419364;