rs12411657

Variant names:

• chr10-69796554-C-T
• rs12411657

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 0.289 in 152,178 control chromosomes in the GnomAD database, including 6,900 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 0.29 (6900 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 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: 0.289 AC: 43909 AN: 152060 Hom.: 6897 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.289 AC: 43921 AN: 152178 Hom.: 6900 Cov.: 33 AF XY: 0.285 AC XY: 21186 AN XY: 74384

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.310

Alfa AF: 0.347 Hom.: 15213

Bravo AF: 0.291

Asia WGS AF: 0.281 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12411657; hg19: chr10-71556310;