rs1354470

Positions:

• chr12-60408140-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 0.589 in 152,044 control chromosomes in the GnomAD database, including 28,608 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 0.59 (28608 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.551

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89439 AN: 151926 Hom.: 28551 Cov.: 33

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.589 AC: 89555 AN: 152044 Hom.: 28608 Cov.: 33 AF XY: 0.585 AC XY: 43492 AN XY: 74318

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.564

Alfa AF: 0.534 Hom.: 3890

Bravo AF: 0.608

Asia WGS AF: 0.496 AC: 1728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1354470; hg19: chr12-60801921;