5-19460543-T-G

Variant names:

• chr5-19460543-T-G
• rs377291

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 0.512 in 151,826 control chromosomes in the GnomAD database, including 21,414 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 0.51 (21414 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.598 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: 0.512 AC: 77669 AN: 151708 Hom.: 21415 Cov.: 33

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.512 AC: 77668 AN: 151826 Hom.: 21414 Cov.: 33 AF XY: 0.512 AC XY: 37989 AN XY: 74182

African (AFR) AF: 0.294 AC: 12174 AN: 41454

American (AMR) AF: 0.609 AC: 9286 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2096 AN: 3464

East Asian (EAS) AF: 0.583 AC: 2998 AN: 5142

South Asian (SAS) AF: 0.518 AC: 2501 AN: 4824

European-Finnish (FIN) AF: 0.565 AC: 5928 AN: 10494

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40785 AN: 67880

Other (OTH) AF: 0.524 AC: 1105 AN: 2110

Alfa AF: 0.419 Hom.: 1378

Bravo AF: 0.511

Asia WGS AF: 0.564 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.30
DANN	Benign	0.39
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs377291; hg19: chr5-19460652;