rs12804004

Variant names:

• chr11-1221069-T-G
• rs12804004

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 0.491 in 151,914 control chromosomes in the GnomAD database, including 19,033 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 0.49 (19033 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.559 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: 0.491 AC: 74515 AN: 151796 Hom.: 19035 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.491 AC: 74541 AN: 151914 Hom.: 19033 Cov.: 33 AF XY: 0.489 AC XY: 36315 AN XY: 74234

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.516

Alfa AF: 0.522 Hom.: 4793

Bravo AF: 0.486

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.35
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: rs12804004; hg19: chr11-1242299;