11-570072-T-C

Variant names:

• chr11-570072-T-C
• rs10902173

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 0.495 in 152,040 control chromosomes in the GnomAD database, including 20,607 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 0.49 (20607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75219 AN: 151922 Hom.: 20613 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.495 AC: 75218 AN: 152040 Hom.: 20607 Cov.: 32 AF XY: 0.500 AC XY: 37179 AN XY: 74304

African (AFR) AF: 0.243 AC: 10081 AN: 41484

American (AMR) AF: 0.462 AC: 7053 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2299 AN: 3472

East Asian (EAS) AF: 0.710 AC: 3636 AN: 5124

South Asian (SAS) AF: 0.607 AC: 2930 AN: 4824

European-Finnish (FIN) AF: 0.674 AC: 7131 AN: 10584

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40282 AN: 67960

Other (OTH) AF: 0.519 AC: 1097 AN: 2112

Alfa AF: 0.526 Hom.: 7952

Bravo AF: 0.470

Asia WGS AF: 0.591 AC: 2057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.32
DANN	Benign	0.70
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10902173; hg19: chr11-570072;