rs4238010

chr12-4009151-G-Achr12-4009151-G-Cchr12-4009151-G-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 0.832 in 152,182 control chromosomes in the GnomAD database, including 53,290 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 0.83 (53290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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: 0.832 AC: 126497 AN: 152064 Hom.: 53254 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.832 AC: 126586 AN: 152182 Hom.: 53290 Cov.: 32 AF XY: 0.834 AC XY: 62051 AN XY: 74402

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.919

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.867

Alfa AF: 0.878 Hom.: 128952

Bravo AF: 0.832

Asia WGS AF: 0.924 AC: 3214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.0040
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4238010; hg19: chr12-4118317;