rs12699683

Positions:

• chr7-15093502-G-T

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 0.083 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0660

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0291

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.0421

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.0735

Gnomad4 OTH AF: 0.0764

Alfa AF: 0.0727 Hom.: 622

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12699683; hg19: chr7-15133127;