rs6489785

Variant names:

• chr12-120925921-T-C
• rs6489785

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;