5-62689026-A-G

Position:

• chr5-62689026-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 0.189 in 152,152 control chromosomes in the GnomAD database, including 2,887 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 0.19 (2887 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28780 AN: 152034 Hom.: 2877 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.189 AC: 28820 AN: 152152 Hom.: 2887 Cov.: 31 AF XY: 0.186 AC XY: 13873 AN XY: 74390

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.182

Alfa AF: 0.184 Hom.: 1561

Bravo AF: 0.194

Asia WGS AF: 0.219 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.74
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1423386; hg19: chr5-61984853;