11-5008473-C-T

Variant names:

• chr11-5008473-C-T
• rs2445284

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 0.561 in 151,884 control chromosomes in the GnomAD database, including 24,434 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 0.56 (24434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85038 AN: 151764 Hom.: 24392 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.561 AC: 85140 AN: 151884 Hom.: 24434 Cov.: 32 AF XY: 0.558 AC XY: 41403 AN XY: 74216

African (AFR) AF: 0.667 AC: 27638 AN: 41428

American (AMR) AF: 0.566 AC: 8638 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2033 AN: 3468

East Asian (EAS) AF: 0.232 AC: 1196 AN: 5164

South Asian (SAS) AF: 0.525 AC: 2522 AN: 4808

European-Finnish (FIN) AF: 0.519 AC: 5451 AN: 10498

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35740 AN: 67932

Other (OTH) AF: 0.570 AC: 1207 AN: 2116

Alfa AF: 0.532 Hom.: 58967

Bravo AF: 0.570

Asia WGS AF: 0.406 AC: 1411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2445284; hg19: chr11-5029703;