rs2870784

Variant names:

• chr12-66088600-A-C
• rs2870784

Your query was ambiguous. Multiple possible variants found:

• chr12-66088600-A-C
• chr12-66088600-A-G
• chr12-66088600-A-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 0.773 in 152,174 control chromosomes in the GnomAD database, including 46,266 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 0.77 (46266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 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: 0.773 AC: 117502 AN: 152056 Hom.: 46217 Cov.: 32

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.773 AC: 117609 AN: 152174 Hom.: 46266 Cov.: 32 AF XY: 0.771 AC XY: 57391 AN XY: 74394

African (AFR) AF: 0.910 AC: 37825 AN: 41546

American (AMR) AF: 0.630 AC: 9609 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2793 AN: 3470

East Asian (EAS) AF: 0.892 AC: 4607 AN: 5164

South Asian (SAS) AF: 0.756 AC: 3647 AN: 4824

European-Finnish (FIN) AF: 0.708 AC: 7495 AN: 10588

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49089 AN: 68006

Other (OTH) AF: 0.745 AC: 1573 AN: 2112

Alfa AF: 0.697 Hom.: 7220

Bravo AF: 0.771

Asia WGS AF: 0.812 AC: 2823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	11
DANN	Benign	0.53
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs2870784; hg19: chr12-66482380;