rs12417955

Variant names:

• chr11-1262997-A-G
• rs12417955

Your query was ambiguous. Multiple possible variants found:

• chr11-1262997-A-G
• chr11-1262997-A-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 0.535 in 517,910 control chromosomes in the GnomAD database, including 74,904 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 0.54 (22376 hom., cov: 33)
  • Exomes 𝑓: 0.53 (52528 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 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: 0.540 AC: 82030 AN: 151880 Hom.: 22342 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.545

GnomAD3 exomes AF: 0.549 AC: 125515 AN: 228708 Hom.: 34900 AF XY: 0.541 AC XY: 68118 AN XY: 125952

Gnomad AFR exome AF: 0.559

Gnomad AMR exome AF: 0.622

Gnomad ASJ exome AF: 0.544

Gnomad EAS exome AF: 0.671

Gnomad SAS exome AF: 0.509

Gnomad FIN exome AF: 0.576

Gnomad NFE exome AF: 0.509

Gnomad OTH exome AF: 0.542

GnomAD4 exome AF: 0.533 AC: 194950 AN: 365912 Hom.: 52528 Cov.: 0 AF XY: 0.526 AC XY: 109335 AN XY: 207946

Gnomad4 AFR exome AF: 0.559

Gnomad4 AMR exome AF: 0.622

Gnomad4 ASJ exome AF: 0.539

Gnomad4 EAS exome AF: 0.673

Gnomad4 SAS exome AF: 0.508

Gnomad4 FIN exome AF: 0.575

Gnomad4 NFE exome AF: 0.507

Gnomad4 OTH exome AF: 0.528

GnomAD4 genome AF: 0.540 AC: 82116 AN: 151998 Hom.: 22376 Cov.: 33 AF XY: 0.546 AC XY: 40529 AN XY: 74290

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.548

Alfa AF: 0.512 Hom.: 10280

Bravo AF: 0.543

Asia WGS AF: 0.622 AC: 2165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12417955; hg19: chr11-1284227;