rs10923825

chr1-119448806-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;