rs1345541

Variant names:

• chr12-105973800-T-C
• rs1345541

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 0.0223 in 152,264 control chromosomes in the GnomAD database, including 99 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 0.022 (99 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 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: 0.0222 AC: 3381 AN: 152146 Hom.: 95 Cov.: 32

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.00801

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0223 AC: 3394 AN: 152264 Hom.: 99 Cov.: 32 AF XY: 0.0239 AC XY: 1780 AN XY: 74440

Gnomad4 AFR AF: 0.0279

Gnomad4 AMR AF: 0.0322

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0654

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.00801

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.0161 Hom.: 7

Bravo AF: 0.0241

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1345541; hg19: chr12-106367578;