5-31020414-A-G

Variant names:

• chr5-31020414-A-G
• rs6888304

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 0.291 in 152,100 control chromosomes in the GnomAD database, including 6,737 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 0.29 (6737 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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: 0.291 AC: 44182 AN: 151982 Hom.: 6729 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.291 AC: 44215 AN: 152100 Hom.: 6737 Cov.: 33 AF XY: 0.287 AC XY: 21353 AN XY: 74354

African (AFR) AF: 0.360 AC: 14940 AN: 41478

American (AMR) AF: 0.206 AC: 3140 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1386 AN: 5180

South Asian (SAS) AF: 0.106 AC: 514 AN: 4828

European-Finnish (FIN) AF: 0.319 AC: 3376 AN: 10580

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19299 AN: 67972

Other (OTH) AF: 0.244 AC: 514 AN: 2110

Alfa AF: 0.282 Hom.: 18073

Bravo AF: 0.286

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.57

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6888304; hg19: chr5-31020521;