rs1354470

Variant names:

• chr12-60408140-T-C
• rs1354470

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;