rs11000828

Variant names:

• chr10-73973541-A-G
• rs11000828

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 0.416 in 152,044 control chromosomes in the GnomAD database, including 14,547 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 0.42 (14547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 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: 0.416 AC: 63272 AN: 151926 Hom.: 14548 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.0366

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.416 AC: 63273 AN: 152044 Hom.: 14547 Cov.: 32 AF XY: 0.405 AC XY: 30099 AN XY: 74330

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.0363

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.456

Alfa AF: 0.509 Hom.: 26079

Bravo AF: 0.418

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.99
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11000828; hg19: chr10-75733299;