rs12701769

Positions:

• chr7-39814031-A-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;