10-90697125-G-T

Position:

• chr10-90697125-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.212 in 152,118 control chromosomes in the GnomAD database, including 4,169 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 0.21 (4169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32232 AN: 152000 Hom.: 4161 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0636

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.212 AC: 32271 AN: 152118 Hom.: 4169 Cov.: 32 AF XY: 0.205 AC XY: 15282 AN XY: 74376

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0637

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.200

Alfa AF: 0.175 Hom.: 1194

Bravo AF: 0.222

Asia WGS AF: 0.0600 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11186275; hg19: chr10-92456882;