rs12810703

Variant names:

• chr12-18917759-G-T
• rs12810703

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 0.249 in 152,026 control chromosomes in the GnomAD database, including 5,854 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 0.25 (5854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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: 0.249 AC: 37856 AN: 151908 Hom.: 5845 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.249 AC: 37900 AN: 152026 Hom.: 5854 Cov.: 32 AF XY: 0.255 AC XY: 18955 AN XY: 74340

African (AFR) AF: 0.391 AC: 16213 AN: 41440

American (AMR) AF: 0.328 AC: 5014 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3468

East Asian (EAS) AF: 0.510 AC: 2630 AN: 5152

South Asian (SAS) AF: 0.218 AC: 1046 AN: 4806

European-Finnish (FIN) AF: 0.145 AC: 1536 AN: 10596

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9784 AN: 67988

Other (OTH) AF: 0.252 AC: 530 AN: 2106

Alfa AF: 0.192 Hom.: 3969

Bravo AF: 0.274

Asia WGS AF: 0.358 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.92
DANN	Benign	0.35
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs12810703; hg19: chr12-19070693;