rs7923382

Variant names:

• chr10-124887934-T-C
• rs7923382

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 0.194 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.150 AC: 6204 AN: 41492

American (AMR) AF: 0.149 AC: 2284 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3468

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5172

South Asian (SAS) AF: 0.0771 AC: 372 AN: 4826

European-Finnish (FIN) AF: 0.351 AC: 3700 AN: 10554

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15959 AN: 67974

Other (OTH) AF: 0.159 AC: 336 AN: 2116

Alfa AF: 0.202 Hom.: 1163

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
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs7923382; hg19: chr10-126576503;