rs10923825

Variant names:

• chr1-119448806-T-C
• rs10923825

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 0.142 in 152,148 control chromosomes in the GnomAD database, including 2,208 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 (2208 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 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: 0.142 AC: 21543 AN: 152030 Hom.: 2204 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0675

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0324

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0793

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.142 AC: 21574 AN: 152148 Hom.: 2208 Cov.: 33 AF XY: 0.141 AC XY: 10452 AN XY: 74390

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0677

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0324

Gnomad4 NFE AF: 0.0793

Gnomad4 OTH AF: 0.145

Alfa AF: 0.0962 Hom.: 1602

Bravo AF: 0.157

Asia WGS AF: 0.106 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10923825; hg19: chr1-119991429;