chr10-117989592-T-C

Variant names:

• chr10-117989592-T-C
• rs12218935

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 0.455 in 152,142 control chromosomes in the GnomAD database, including 18,553 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 0.46 (18553 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69268 AN: 152022 Hom.: 18546 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.455 AC: 69291 AN: 152142 Hom.: 18553 Cov.: 32 AF XY: 0.455 AC XY: 33845 AN XY: 74362

African (AFR) AF: 0.195 AC: 8089 AN: 41504

American (AMR) AF: 0.414 AC: 6337 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1902 AN: 3464

East Asian (EAS) AF: 0.169 AC: 873 AN: 5176

South Asian (SAS) AF: 0.584 AC: 2815 AN: 4824

European-Finnish (FIN) AF: 0.644 AC: 6816 AN: 10582

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40837 AN: 67990

Other (OTH) AF: 0.489 AC: 1029 AN: 2106

Alfa AF: 0.546 Hom.: 29377

Bravo AF: 0.423

Asia WGS AF: 0.380 AC: 1323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.21
DANN	Benign	0.55
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12218935; hg19: chr10-119749103;