rs7923382

chr10-124887934-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 0.194 in 152,090 control chromosomes in the GnomAD database, including 3,258 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 0.19 (3258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

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 (NFE) allele frequency at 95% confidence interval = 0.232 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: 0.194 AC: 29484 AN: 151972 Hom.: 3259 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0770

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.194 AC: 29492 AN: 152090 Hom.: 3258 Cov.: 32 AF XY: 0.194 AC XY: 14450 AN XY: 74346

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0771

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.159

Alfa AF: 0.223 Hom.: 667

Bravo AF: 0.173

Asia WGS AF: 0.0470 AC: 168 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	3.2
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7923382; hg19: chr10-126576503;