chr10-107616211-T-A

Variant names:

• chr10-107616211-T-A
• rs2099803

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 0.447 in 151,914 control chromosomes in the GnomAD database, including 15,743 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 0.45 (15743 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 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: 0.448 AC: 67977 AN: 151796 Hom.: 15746 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.447 AC: 67979 AN: 151914 Hom.: 15743 Cov.: 31 AF XY: 0.443 AC XY: 32872 AN XY: 74254

African (AFR) AF: 0.367 AC: 15219 AN: 41436

American (AMR) AF: 0.446 AC: 6801 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3466

East Asian (EAS) AF: 0.208 AC: 1079 AN: 5180

South Asian (SAS) AF: 0.304 AC: 1461 AN: 4806

European-Finnish (FIN) AF: 0.504 AC: 5309 AN: 10542

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35190 AN: 67920

Other (OTH) AF: 0.452 AC: 955 AN: 2114

Alfa AF: 0.482 Hom.: 2250

Bravo AF: 0.442

Asia WGS AF: 0.261 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.37

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2099803; hg19: chr10-109375969;