rs1345541

Positions:

• chr12-105973800-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 0.0223 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;