5-31020414-A-G

Position:

• chr5-31020414-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.244

Alfa AF: 0.280 Hom.: 5385

Bravo AF: 0.286

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6888304; hg19: chr5-31020521;