5-98432782-A-G

Variant names:

• chr5-98432782-A-G
• rs1563317

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 0.595 in 152,052 control chromosomes in the GnomAD database, including 28,055 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 0.60 (28055 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 6 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 = 0.778 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: 0.595 AC: 90427 AN: 151934 Hom.: 28020 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.595 AC: 90508 AN: 152052 Hom.: 28055 Cov.: 32 AF XY: 0.588 AC XY: 43683 AN XY: 74326

African (AFR) AF: 0.785 AC: 32595 AN: 41496

American (AMR) AF: 0.500 AC: 7648 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1745 AN: 3464

East Asian (EAS) AF: 0.434 AC: 2241 AN: 5160

South Asian (SAS) AF: 0.599 AC: 2876 AN: 4804

European-Finnish (FIN) AF: 0.449 AC: 4740 AN: 10568

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.541 AC: 36755 AN: 67964

Other (OTH) AF: 0.557 AC: 1178 AN: 2114

Alfa AF: 0.560 Hom.: 74858

Bravo AF: 0.608

Asia WGS AF: 0.570 AC: 1980 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	3.7
DANN	Benign	0.47
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs1563317; hg19: chr5-97768486;