rs12534697

Variant names:

• chr7-69074845-G-C
• rs12534697

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 0.164 in 152,088 control chromosomes in the GnomAD database, including 2,305 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 (2305 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 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: 0.164 AC: 24951 AN: 151970 Hom.: 2300 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.164 AC: 24962 AN: 152088 Hom.: 2305 Cov.: 32 AF XY: 0.170 AC XY: 12623 AN XY: 74358

African (AFR) AF: 0.120 AC: 4961 AN: 41496

American (AMR) AF: 0.259 AC: 3945 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1623 AN: 5168

South Asian (SAS) AF: 0.239 AC: 1154 AN: 4820

European-Finnish (FIN) AF: 0.169 AC: 1783 AN: 10570

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.143 AC: 9705 AN: 67996

Other (OTH) AF: 0.183 AC: 386 AN: 2106

Alfa AF: 0.142 Hom.: 174

Bravo AF: 0.170

Asia WGS AF: 0.314 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.47
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs12534697; hg19: chr7-68539832;