5-123296729-G-T

Variant names:

• chr5-123296729-G-T
• rs2897737

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 0.209 in 151,890 control chromosomes in the GnomAD database, including 3,508 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 0.21 (3508 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 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: 0.209 AC: 31672 AN: 151772 Hom.: 3508 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.209 AC: 31693 AN: 151890 Hom.: 3508 Cov.: 33 AF XY: 0.207 AC XY: 15339 AN XY: 74222

African (AFR) AF: 0.275 AC: 11405 AN: 41448

American (AMR) AF: 0.205 AC: 3123 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 443 AN: 3464

East Asian (EAS) AF: 0.171 AC: 885 AN: 5182

South Asian (SAS) AF: 0.170 AC: 822 AN: 4822

European-Finnish (FIN) AF: 0.181 AC: 1914 AN: 10554

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.184 AC: 12498 AN: 67870

Other (OTH) AF: 0.205 AC: 430 AN: 2102

Alfa AF: 0.186 Hom.: 10503

Bravo AF: 0.211

Asia WGS AF: 0.185 AC: 641 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.33
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs2897737; hg19: chr5-122632423;