rs10921078

Variant names:

• chr1-192089892-G-A
• rs10921078

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0320 AC: 1323 AN: 41342

American (AMR) AF: 0.0942 AC: 1426 AN: 15130

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3456

East Asian (EAS) AF: 0.00640 AC: 33 AN: 5156

South Asian (SAS) AF: 0.0315 AC: 151 AN: 4796

European-Finnish (FIN) AF: 0.185 AC: 1909 AN: 10346

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11708 AN: 67582

Other (OTH) AF: 0.125 AC: 261 AN: 2082

Alfa AF: 0.152 Hom.: 3296

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10921078; hg19: chr1-192059022;