rs4018511

chr12-48961253-G-A

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 0.0825 in 152,274 control chromosomes in the GnomAD database, including 978 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 0.082 (978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 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: 0.0823 AC: 12527 AN: 152156 Hom.: 966 Cov.: 32

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.0426

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.0871

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

GnomAD4 genome AF: 0.0825 AC: 12555 AN: 152274 Hom.: 978 Cov.: 32 AF XY: 0.0880 AC XY: 6554 AN XY: 74448

Gnomad4 AFR AF: 0.0186

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.0426

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.0817

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0709

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.0834 Hom.: 902

Bravo AF: 0.0919

Asia WGS AF: 0.190 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	11
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4018511; hg19: chr12-49355036;