rs12699683

Variant names:

• chr7-15093502-G-T
• rs12699683

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 0.083 in 152,060 control chromosomes in the GnomAD database, including 677 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 0.083 (677 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 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: 0.0830 AC: 12611 AN: 151942 Hom.: 680 Cov.: 32

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.0425

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0735

Gnomad OTH AF: 0.0762

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

GnomAD4 genome AF: 0.0830 AC: 12623 AN: 152060 Hom.: 677 Cov.: 32 AF XY: 0.0870 AC XY: 6468 AN XY: 74352

African (AFR) AF: 0.0660 AC: 2742 AN: 41520

American (AMR) AF: 0.124 AC: 1886 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0291 AC: 101 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1046 AN: 5152

South Asian (SAS) AF: 0.0421 AC: 203 AN: 4820

European-Finnish (FIN) AF: 0.136 AC: 1433 AN: 10562

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0735 AC: 4994 AN: 67966

Other (OTH) AF: 0.0764 AC: 161 AN: 2108

Alfa AF: 0.0742 Hom.: 922

Bravo AF: 0.0829

Asia WGS AF: 0.111 AC: 384 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.48
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs12699683; hg19: chr7-15133127;