rs309038

Variant names:

• chr12-28847493-T-A
• rs309038

Your query was ambiguous. Multiple possible variants found:

• chr12-28847493-T-A
• chr12-28847493-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 0.936 in 151,798 control chromosomes in the GnomAD database, including 66,937 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 0.94 (66937 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 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: 0.936 AC: 142025 AN: 151680 Hom.: 66892 Cov.: 30

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.986

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.959

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

GnomAD4 genome AF: 0.936 AC: 142129 AN: 151798 Hom.: 66937 Cov.: 30 AF XY: 0.933 AC XY: 69211 AN XY: 74198

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.993

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.986

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.959

Alfa AF: 0.957 Hom.: 8680

Bravo AF: 0.924

Asia WGS AF: 0.803 AC: 2791 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs309038; hg19: chr12-29000426;