rs853516

Variant names:

• chr12-25839609-C-A
• rs853516

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 0.18 in 152,178 control chromosomes in the GnomAD database, including 2,993 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 0.18 (2993 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 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: 0.180 AC: 27311 AN: 152060 Hom.: 2981 Cov.: 33

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.180 AC: 27364 AN: 152178 Hom.: 2993 Cov.: 33 AF XY: 0.184 AC XY: 13694 AN XY: 74388

African (AFR) AF: 0.267 AC: 11075 AN: 41522

American (AMR) AF: 0.223 AC: 3412 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 411 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1825 AN: 5182

South Asian (SAS) AF: 0.251 AC: 1209 AN: 4824

European-Finnish (FIN) AF: 0.129 AC: 1364 AN: 10598

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7590 AN: 67980

Other (OTH) AF: 0.182 AC: 384 AN: 2112

Alfa AF: 0.130 Hom.: 2553

Bravo AF: 0.192

Asia WGS AF: 0.287 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.81
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs853516; hg19: chr12-25992543;