rs12804004

Positions:

• chr11-1221069-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;