chr5-119426330-A-G

Variant names:

• chr5-119426330-A-G
• rs2455466

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 0.748 in 152,136 control chromosomes in the GnomAD database, including 43,709 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 0.75 (43709 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 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: 0.748 AC: 113698 AN: 152018 Hom.: 43655 Cov.: 32

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.748 AC: 113807 AN: 152136 Hom.: 43709 Cov.: 32 AF XY: 0.745 AC XY: 55406 AN XY: 74354

African (AFR) AF: 0.936 AC: 38860 AN: 41526

American (AMR) AF: 0.642 AC: 9811 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2098 AN: 3472

East Asian (EAS) AF: 0.587 AC: 3038 AN: 5176

South Asian (SAS) AF: 0.770 AC: 3715 AN: 4822

European-Finnish (FIN) AF: 0.670 AC: 7083 AN: 10570

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46870 AN: 67966

Other (OTH) AF: 0.713 AC: 1505 AN: 2112

Alfa AF: 0.710 Hom.: 50621

Bravo AF: 0.748

Asia WGS AF: 0.674 AC: 2349 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.57
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs2455466; hg19: chr5-118762025;