rs11000828

Positions:

• chr10-73973541-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;