chr11-23645970-A-C

Variant names:

• chr11-23645970-A-C
• rs1519414

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 0.252 in 151,974 control chromosomes in the GnomAD database, including 5,568 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 0.25 (5568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.363 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: 0.253 AC: 38380 AN: 151856 Hom.: 5576 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.252 AC: 38369 AN: 151974 Hom.: 5568 Cov.: 32 AF XY: 0.253 AC XY: 18801 AN XY: 74250

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.288

Alfa AF: 0.304 Hom.: 9255

Bravo AF: 0.244

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.52
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1519414; hg19: chr11-23667516;