rs12295403

Positions:

• chr11-18668106-C-A
• chr11-18668106-C-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 0.257 in 152,070 control chromosomes in the GnomAD database, including 5,919 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 0.26 (5919 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39155 AN: 151952 Hom.: 5924 Cov.: 32

Gnomad AFR AF: 0.0953

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.257 AC: 39151 AN: 152070 Hom.: 5919 Cov.: 32 AF XY: 0.255 AC XY: 18945 AN XY: 74344

Gnomad4 AFR AF: 0.0953

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.297

Alfa AF: 0.328 Hom.: 12249

Bravo AF: 0.248

Asia WGS AF: 0.235 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12295403; hg19: chr11-18689653;