rs215340

chr12-47338855-A-Gchr12-47338855-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 0.814 in 152,140 control chromosomes in the GnomAD database, including 50,798 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 0.81 (50798 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 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: 0.814 AC: 123750 AN: 152022 Hom.: 50760 Cov.: 31

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.814 AC: 123844 AN: 152140 Hom.: 50798 Cov.: 31 AF XY: 0.814 AC XY: 60557 AN XY: 74392

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.788

Alfa AF: 0.764 Hom.: 89060

Bravo AF: 0.819

Asia WGS AF: 0.828 AC: 2878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.9
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs215340; hg19: chr12-47732638;