rs10861553

chr12-106059036-G-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 0.482 in 152,074 control chromosomes in the GnomAD database, including 18,175 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 0.48 (18175 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.584 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: 0.482 AC: 73196 AN: 151956 Hom.: 18154 Cov.: 33

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.482 AC: 73257 AN: 152074 Hom.: 18175 Cov.: 33 AF XY: 0.481 AC XY: 35761 AN XY: 74328

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.481

Alfa AF: 0.501 Hom.: 4266

Bravo AF: 0.481

Asia WGS AF: 0.453 AC: 1573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.49
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10861553; hg19: chr12-106452814;