rs12701769

Variant names:

• chr7-39814031-A-C
• rs12701769

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 0.165 in 152,148 control chromosomes in the GnomAD database, including 2,302 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 0.16 (2302 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 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: 0.165 AC: 25014 AN: 152030 Hom.: 2299 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.165 AC: 25046 AN: 152148 Hom.: 2302 Cov.: 32 AF XY: 0.165 AC XY: 12239 AN XY: 74384

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.199

Alfa AF: 0.192 Hom.: 526

Bravo AF: 0.170

Asia WGS AF: 0.0830 AC: 291 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	4.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12701769; hg19: chr7-39853630;