5-119424720-T-G

Variant names:

• chr5-119424720-T-G
• rs2451818

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 0.404 in 152,084 control chromosomes in the GnomAD database, including 13,166 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 0.40 (13166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 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: 0.404 AC: 61467 AN: 151966 Hom.: 13164 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.404 AC: 61492 AN: 152084 Hom.: 13166 Cov.: 32 AF XY: 0.399 AC XY: 29623 AN XY: 74332

African (AFR) AF: 0.327 AC: 13583 AN: 41496

American (AMR) AF: 0.418 AC: 6384 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3466

East Asian (EAS) AF: 0.0760 AC: 394 AN: 5186

South Asian (SAS) AF: 0.448 AC: 2164 AN: 4826

European-Finnish (FIN) AF: 0.385 AC: 4063 AN: 10558

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.476 AC: 32319 AN: 67954

Other (OTH) AF: 0.412 AC: 872 AN: 2114

Alfa AF: 0.442 Hom.: 7500

Bravo AF: 0.398

Asia WGS AF: 0.297 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2451818; hg19: chr5-118760415;