rs12608723

chr19-33326227-A-Gchr19-33326227-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.23 in 151,930 control chromosomes in the GnomAD database, including 5,174 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 0.23 (5174 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34834 AN: 151810 Hom.: 5153 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.230 AC: 34894 AN: 151930 Hom.: 5174 Cov.: 31 AF XY: 0.230 AC XY: 17097 AN XY: 74240

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.210

Alfa AF: 0.161 Hom.: 1496

Bravo AF: 0.246

Asia WGS AF: 0.199 AC: 696 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	3.1
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12608723; hg19: chr19-33817133;