rs1544396

Positions:

• chr12-111625071-T-C

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 0.26 in 151,932 control chromosomes in the GnomAD database, including 6,795 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 0.26 (6795 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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: 0.260 AC: 39504 AN: 151814 Hom.: 6800 Cov.: 30

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.260 AC: 39539 AN: 151932 Hom.: 6795 Cov.: 30 AF XY: 0.264 AC XY: 19637 AN XY: 74258

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.274

Alfa AF: 0.199 Hom.: 7562

Bravo AF: 0.279

Asia WGS AF: 0.528 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.29
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1544396; hg19: chr12-112062875;