rs10490068

Variant names:

• chr2-60259112-A-G
• rs10490068

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 0.0549 in 152,256 control chromosomes in the GnomAD database, including 440 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 0.055 (440 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 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: 0.0549 AC: 8346 AN: 152138 Hom.: 440 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0231

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0342

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0549 AC: 8365 AN: 152256 Hom.: 440 Cov.: 33 AF XY: 0.0539 AC XY: 4013 AN XY: 74452

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0231

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0342

Gnomad4 NFE AF: 0.0210

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0417 Hom.: 40

Bravo AF: 0.0583

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490068; hg19: chr2-60486247;