rs10921078

Positions:

• chr1-192089892-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;