rs10998046

Variant names:

• chr10-68269641-A-G
• rs10998046

Your query was ambiguous. Multiple possible variants found:

• chr10-68269641-A-G
• chr10-68269641-A-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 0.139 in 152,162 control chromosomes in the GnomAD database, including 1,962 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 0.14 (1962 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624

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 (SAS) allele frequency at 95% confidence interval = 0.228 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: 0.139 AC: 21103 AN: 152044 Hom.: 1961 Cov.: 32

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.139 AC: 21111 AN: 152162 Hom.: 1962 Cov.: 32 AF XY: 0.144 AC XY: 10727 AN XY: 74396

Gnomad4 AFR AF: 0.0314

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.142

Alfa AF: 0.163 Hom.: 376

Bravo AF: 0.136

Asia WGS AF: 0.173 AC: 602 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	0.56
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10998046; hg19: chr10-70029398;