rs11000101

Variant names:

• chr10-71933970-G-A
• rs11000101

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 0.188 in 152,158 control chromosomes in the GnomAD database, including 2,885 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 (2885 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.226 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: 0.188 AC: 28578 AN: 152040 Hom.: 2881 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.188 AC: 28601 AN: 152158 Hom.: 2885 Cov.: 32 AF XY: 0.184 AC XY: 13666 AN XY: 74376

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.197

Alfa AF: 0.216 Hom.: 1709

Bravo AF: 0.190

Asia WGS AF: 0.158 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11000101; hg19: chr10-73693728;