rs12411657

Positions:

• chr10-69796554-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;