rs706824

Variant names:

• chr12-51925467-A-G
• rs706824

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 0.344 in 151,868 control chromosomes in the GnomAD database, including 9,985 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 0.34 (9985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 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: 0.344 AC: 52198 AN: 151746 Hom.: 9960 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.344 AC: 52263 AN: 151868 Hom.: 9985 Cov.: 32 AF XY: 0.342 AC XY: 25429 AN XY: 74254

African (AFR) AF: 0.512 AC: 21225 AN: 41424

American (AMR) AF: 0.250 AC: 3812 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3464

East Asian (EAS) AF: 0.483 AC: 2495 AN: 5166

South Asian (SAS) AF: 0.267 AC: 1283 AN: 4800

European-Finnish (FIN) AF: 0.291 AC: 3072 AN: 10560

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18133 AN: 67878

Other (OTH) AF: 0.338 AC: 712 AN: 2108

Alfa AF: 0.296 Hom.: 22887

Bravo AF: 0.348

Asia WGS AF: 0.375 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.74
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs706824; hg19: chr12-52319251;