rs4238010

Variant names:

• chr12-4009151-G-A
• rs4238010

Your query was ambiguous. Multiple possible variants found:

• chr12-4009151-G-A
• chr12-4009151-G-C
• chr12-4009151-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;