rs12459044

Variant names:

• chr19-7667520-C-G
• rs12459044

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 0.108 in 151,344 control chromosomes in the GnomAD database, including 1,111 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 0.11 (1111 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.153 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: 0.109 AC: 16408 AN: 151224 Hom.: 1108 Cov.: 30

Gnomad AFR AF: 0.0268

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.108 AC: 16414 AN: 151344 Hom.: 1111 Cov.: 30 AF XY: 0.110 AC XY: 8142 AN XY: 73926

Gnomad4 AFR AF: 0.0268

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.0395

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.115

Alfa AF: 0.126 Hom.: 166

Bravo AF: 0.106

Asia WGS AF: 0.0790 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12459044; hg19: chr19-7732406;