5-84920196-T-C

Variant names:

• chr5-84920196-T-C
• rs1605987

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 0.862 in 152,218 control chromosomes in the GnomAD database, including 56,685 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 0.86 (56685 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 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: 0.861 AC: 131031 AN: 152100 Hom.: 56638 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.862 AC: 131137 AN: 152218 Hom.: 56685 Cov.: 32 AF XY: 0.858 AC XY: 63823 AN XY: 74404

African (AFR) AF: 0.938 AC: 38992 AN: 41564

American (AMR) AF: 0.890 AC: 13604 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2856 AN: 3472

East Asian (EAS) AF: 0.768 AC: 3965 AN: 5162

South Asian (SAS) AF: 0.769 AC: 3710 AN: 4824

European-Finnish (FIN) AF: 0.801 AC: 8478 AN: 10590

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56698 AN: 68008

Other (OTH) AF: 0.859 AC: 1815 AN: 2112

Alfa AF: 0.856 Hom.: 9281

Bravo AF: 0.871

Asia WGS AF: 0.790 AC: 2750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.29
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1605987; hg19: chr5-84216014;