rs10861553

Variant names:

• chr12-106059036-G-T
• rs10861553

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.358 AC: 14851 AN: 41488

American (AMR) AF: 0.595 AC: 9091 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1698 AN: 3472

East Asian (EAS) AF: 0.421 AC: 2177 AN: 5172

South Asian (SAS) AF: 0.476 AC: 2292 AN: 4816

European-Finnish (FIN) AF: 0.505 AC: 5336 AN: 10568

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36182 AN: 67958

Other (OTH) AF: 0.481 AC: 1013 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.49
DANN	Benign	0.34
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs10861553; hg19: chr12-106452814;