rs6489785

Variant names:

• chr12-120925921-T-C
• rs6489785

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 0.686 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
• Publications: 30 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.744 AC: 30824 AN: 41454

American (AMR) AF: 0.775 AC: 11813 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2424 AN: 3466

East Asian (EAS) AF: 0.846 AC: 4380 AN: 5178

South Asian (SAS) AF: 0.822 AC: 3958 AN: 4814

European-Finnish (FIN) AF: 0.640 AC: 6753 AN: 10554

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41778 AN: 67932

Other (OTH) AF: 0.681 AC: 1430 AN: 2100

Alfa AF: 0.611 Hom.: 7184

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
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs6489785; hg19: chr12-121363724;