rs10926796

Variant names:

• chr1-242632712-G-A
• rs10926796

Your query was ambiguous. Multiple possible variants found:

• chr1-242632712-G-A
• chr1-242632712-G-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 0.177 in 152,174 control chromosomes in the GnomAD database, including 2,746 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 0.18 (2746 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 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: 0.177 AC: 26920 AN: 152056 Hom.: 2747 Cov.: 33

Gnomad AFR AF: 0.0758

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0734

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.177 AC: 26928 AN: 152174 Hom.: 2746 Cov.: 33 AF XY: 0.177 AC XY: 13154 AN XY: 74394

Gnomad4 AFR AF: 0.0757

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.0731

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.204

Alfa AF: 0.221 Hom.: 4406

Bravo AF: 0.175

Asia WGS AF: 0.151 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10926796; hg19: chr1-242796014;