rs12319113

Positions:

• chr12-18871624-G-A
• chr12-18871624-G-C
• chr12-18871624-G-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 0.141 in 152,072 control chromosomes in the GnomAD database, including 2,519 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 0.14 (2519 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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: 0.140 AC: 21349 AN: 151954 Hom.: 2512 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0774

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.0875

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.0624

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.141 AC: 21385 AN: 152072 Hom.: 2519 Cov.: 31 AF XY: 0.141 AC XY: 10482 AN XY: 74342

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.0771

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.0643

Gnomad4 SAS AF: 0.0507

Gnomad4 FIN AF: 0.0875

Gnomad4 NFE AF: 0.0624

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0259 Hom.: 25

Bravo AF: 0.151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12319113; hg19: chr12-19024558;