chr10-58189975-C-T

Variant names:

• chr10-58189975-C-T
• rs1199098

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 0.338 in 152,044 control chromosomes in the GnomAD database, including 10,961 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 0.34 (10961 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51378 AN: 151926 Hom.: 10927 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.338 AC: 51466 AN: 152044 Hom.: 10961 Cov.: 32 AF XY: 0.338 AC XY: 25106 AN XY: 74314

African (AFR) AF: 0.607 AC: 25179 AN: 41454

American (AMR) AF: 0.236 AC: 3602 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2304 AN: 5168

South Asian (SAS) AF: 0.276 AC: 1329 AN: 4820

European-Finnish (FIN) AF: 0.220 AC: 2330 AN: 10572

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15095 AN: 67970

Other (OTH) AF: 0.283 AC: 598 AN: 2112

Alfa AF: 0.257 Hom.: 3273

Bravo AF: 0.353

Asia WGS AF: 0.322 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.092
DANN	Benign	0.41
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1199098; hg19: chr10-59949736;