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. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.900 AC: 37312 AN: 41474

American (AMR) AF: 0.869 AC: 13241 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3439 AN: 3462

East Asian (EAS) AF: 0.651 AC: 3344 AN: 5140

South Asian (SAS) AF: 0.905 AC: 4366 AN: 4826

European-Finnish (FIN) AF: 0.986 AC: 10454 AN: 10604

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.985 AC: 66753 AN: 67752

Other (OTH) AF: 0.959 AC: 2018 AN: 2104

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
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs309038; hg19: chr12-29000426;