rs10784749

Positions:

• chr12-69028249-C-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 0.688 in 152,152 control chromosomes in the GnomAD database, including 36,972 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 0.69 (36972 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104583 AN: 152034 Hom.: 36976 Cov.: 33

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.688 AC: 104606 AN: 152152 Hom.: 36972 Cov.: 33 AF XY: 0.692 AC XY: 51499 AN XY: 74380

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.706

Alfa AF: 0.726 Hom.: 5085

Bravo AF: 0.666

Asia WGS AF: 0.634 AC: 2205 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10784749; hg19: chr12-69422029; COSMIC: COSV70149629;