rs11011581

Variant names:

• chr10-19811890-T-C
• rs11011581

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 0.0899 in 152,312 control chromosomes in the GnomAD database, including 787 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 0.090 (787 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0898 AC: 13665 AN: 152194 Hom.: 783 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.0581

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.0831

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

GnomAD4 genome AF: 0.0899 AC: 13700 AN: 152312 Hom.: 787 Cov.: 33 AF XY: 0.0885 AC XY: 6593 AN XY: 74486

African (AFR) AF: 0.155 AC: 6452 AN: 41544

American (AMR) AF: 0.0595 AC: 910 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0591 AC: 205 AN: 3470

East Asian (EAS) AF: 0.0580 AC: 301 AN: 5190

South Asian (SAS) AF: 0.101 AC: 488 AN: 4834

European-Finnish (FIN) AF: 0.0362 AC: 384 AN: 10614

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0686 AC: 4670 AN: 68036

Other (OTH) AF: 0.0888 AC: 188 AN: 2116

Alfa AF: 0.0764 Hom.: 459

Bravo AF: 0.0931

Asia WGS AF: 0.101 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.77
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs11011581; hg19: chr10-20100819;