rs10921078

Variant names:

• chr1-192089892-G-A
• rs10921078

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 0.117 in 151,092 control chromosomes in the GnomAD database, including 1,368 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 0.12 (1368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 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: 0.117 AC: 17619 AN: 150974 Hom.: 1368 Cov.: 32

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.0944

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.00639

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.117 AC: 17609 AN: 151092 Hom.: 1368 Cov.: 32 AF XY: 0.114 AC XY: 8425 AN XY: 73768

Gnomad4 AFR AF: 0.0320

Gnomad4 AMR AF: 0.0942

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.00640

Gnomad4 SAS AF: 0.0315

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.125

Alfa AF: 0.153 Hom.: 947

Bravo AF: 0.108

Asia WGS AF: 0.0410 AC: 143 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10921078; hg19: chr1-192059022;