rs6489785

Positions:

• chr12-120925921-T-C

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 0.686 in 151,952 control chromosomes in the GnomAD database, including 36,271 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 (36271 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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: 0.686 AC: 104191 AN: 151834 Hom.: 36231 Cov.: 31

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.686 AC: 104285 AN: 151952 Hom.: 36271 Cov.: 31 AF XY: 0.698 AC XY: 51810 AN XY: 74258

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.681

Alfa AF: 0.370 Hom.: 384

Bravo AF: 0.698

Asia WGS AF: 0.826 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6489785; hg19: chr12-121363724;