rs12701769

Variant names:

• chr7-39814031-A-C
• rs12701769

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 0.165 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.119 AC: 4935 AN: 41516

American (AMR) AF: 0.260 AC: 3983 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3466

East Asian (EAS) AF: 0.0185 AC: 96 AN: 5182

South Asian (SAS) AF: 0.115 AC: 554 AN: 4816

European-Finnish (FIN) AF: 0.173 AC: 1830 AN: 10582

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12280 AN: 67974

Other (OTH) AF: 0.199 AC: 420 AN: 2114

Alfa AF: 0.190 Hom.: 534

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs12701769; hg19: chr7-39853630;