rs10833173

Variant names:

• chr11-3073275-T-A
• rs10833173

Your query was ambiguous. Multiple possible variants found:

• chr11-3073275-T-A
• chr11-3073275-T-C

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 0.315 in 152,018 control chromosomes in the GnomAD database, including 7,864 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 0.32 (7864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 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: 0.315 AC: 47880 AN: 151900 Hom.: 7851 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.315 AC: 47929 AN: 152018 Hom.: 7864 Cov.: 32 AF XY: 0.317 AC XY: 23576 AN XY: 74284

African (AFR) AF: 0.408 AC: 16914 AN: 41458

American (AMR) AF: 0.242 AC: 3693 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 830 AN: 3470

East Asian (EAS) AF: 0.186 AC: 965 AN: 5184

South Asian (SAS) AF: 0.302 AC: 1454 AN: 4808

European-Finnish (FIN) AF: 0.378 AC: 3987 AN: 10558

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19141 AN: 67956

Other (OTH) AF: 0.262 AC: 552 AN: 2106

Alfa AF: 0.202 Hom.: 450

Bravo AF: 0.308

Asia WGS AF: 0.261 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.27
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10833173; hg19: chr11-3094505;