chr10-100712899-G-C

Variant names:

• chr10-100712899-G-C
• rs10883533

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 0.379 in 151,944 control chromosomes in the GnomAD database, including 13,112 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 0.38 (13112 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57541 AN: 151826 Hom.: 13116 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.379 AC: 57551 AN: 151944 Hom.: 13112 Cov.: 31 AF XY: 0.394 AC XY: 29266 AN XY: 74266

African (AFR) AF: 0.170 AC: 7053 AN: 41488

American (AMR) AF: 0.451 AC: 6888 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3466

East Asian (EAS) AF: 0.951 AC: 4899 AN: 5150

South Asian (SAS) AF: 0.549 AC: 2633 AN: 4798

European-Finnish (FIN) AF: 0.561 AC: 5906 AN: 10534

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27569 AN: 67934

Other (OTH) AF: 0.372 AC: 783 AN: 2106

Alfa AF: 0.391 Hom.: 1574

Bravo AF: 0.360

Asia WGS AF: 0.679 AC: 2358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	6.3
DANN	Benign	0.71
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs10883533; hg19: chr10-102472656;