rs753013

Variant names:

• chr12-28899977-G-A
• rs753013

Your query was ambiguous. Multiple possible variants found:

• chr12-28899977-G-A
• chr12-28899977-G-C
• chr12-28899977-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 0.424 in 151,956 control chromosomes in the GnomAD database, including 14,487 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 0.42 (14487 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.569 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: 0.425 AC: 64479 AN: 151838 Hom.: 14477 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.424 AC: 64503 AN: 151956 Hom.: 14487 Cov.: 31 AF XY: 0.430 AC XY: 31962 AN XY: 74286

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.418

Alfa AF: 0.430 Hom.: 1775

Bravo AF: 0.424

Asia WGS AF: 0.415 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs753013; hg19: chr12-29052910;