rs2660869

Variant names:

• chr12-96085489-G-C
• rs2660869

Your query was ambiguous. Multiple possible variants found:

• chr12-96085489-G-C
• chr12-96085489-G-T

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 0.108 in 152,200 control chromosomes in the GnomAD database, including 923 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 0.11 (923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 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: 0.108 AC: 16352 AN: 152082 Hom.: 916 Cov.: 32

Gnomad AFR AF: 0.0945

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0649

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.108 AC: 16374 AN: 152200 Hom.: 923 Cov.: 32 AF XY: 0.105 AC XY: 7791 AN XY: 74400

African (AFR) AF: 0.0950 AC: 3948 AN: 41538

American (AMR) AF: 0.121 AC: 1851 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.0648 AC: 313 AN: 4832

European-Finnish (FIN) AF: 0.0831 AC: 879 AN: 10578

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8496 AN: 67996

Other (OTH) AF: 0.121 AC: 256 AN: 2112

Alfa AF: 0.0509 Hom.: 53

Bravo AF: 0.110

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.33
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs2660869; hg19: chr12-96479267;