rs11591930

Variant names:

• chr10-70768808-T-A
• rs11591930

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 0.236 in 152,112 control chromosomes in the GnomAD database, including 4,539 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 0.24 (4539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 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: 0.237 AC: 35961 AN: 151994 Hom.: 4543 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.236 AC: 35962 AN: 152112 Hom.: 4539 Cov.: 32 AF XY: 0.236 AC XY: 17577 AN XY: 74372

African (AFR) AF: 0.157 AC: 6513 AN: 41504

American (AMR) AF: 0.277 AC: 4238 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1254 AN: 3468

East Asian (EAS) AF: 0.227 AC: 1174 AN: 5182

South Asian (SAS) AF: 0.144 AC: 695 AN: 4816

European-Finnish (FIN) AF: 0.267 AC: 2819 AN: 10566

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18459 AN: 67984

Other (OTH) AF: 0.248 AC: 524 AN: 2110

Alfa AF: 0.249 Hom.: 598

Bravo AF: 0.238

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.69
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs11591930; hg19: chr10-72528564;