rs309038

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;