rs12295403

Variant names:

• chr11-18668106-C-A
• rs12295403

Your query was ambiguous. Multiple possible variants found:

• chr11-18668106-C-A
• chr11-18668106-C-T

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 0.257 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0953 AC: 3956 AN: 41498

American (AMR) AF: 0.269 AC: 4116 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3472

East Asian (EAS) AF: 0.235 AC: 1217 AN: 5172

South Asian (SAS) AF: 0.269 AC: 1297 AN: 4820

European-Finnish (FIN) AF: 0.283 AC: 2991 AN: 10568

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.341 AC: 23200 AN: 67950

Other (OTH) AF: 0.297 AC: 627 AN: 2110

Alfa AF: 0.315 Hom.: 30332

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs12295403; hg19: chr11-18689653;