13-33817815-T-G

Variant names:

• chr13-33817815-T-G
• rs2147668

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 0.229 in 152,118 control chromosomes in the GnomAD database, including 6,334 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 0.23 (6334 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776
• Publications: 4 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 = 0.472 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: 0.229 AC: 34749 AN: 152000 Hom.: 6305 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0822

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.229 AC: 34835 AN: 152118 Hom.: 6334 Cov.: 32 AF XY: 0.230 AC XY: 17121 AN XY: 74382

African (AFR) AF: 0.477 AC: 19780 AN: 41446

American (AMR) AF: 0.301 AC: 4606 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3464

East Asian (EAS) AF: 0.328 AC: 1699 AN: 5174

South Asian (SAS) AF: 0.219 AC: 1057 AN: 4822

European-Finnish (FIN) AF: 0.0822 AC: 872 AN: 10608

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0850 AC: 5778 AN: 68004

Other (OTH) AF: 0.230 AC: 486 AN: 2116

Alfa AF: 0.154 Hom.: 7648

Bravo AF: 0.262

Asia WGS AF: 0.300 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.57
PhyloP100		-0.78
PromoterAI		-0.019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2147668; hg19: chr13-34391952;