rs665579

Variant names:

• chr5-63515591-A-G
• rs665579

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 0.222 in 152,068 control chromosomes in the GnomAD database, including 3,741 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 0.22 (3741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33733 AN: 151950 Hom.: 3734 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.222 AC: 33751 AN: 152068 Hom.: 3741 Cov.: 32 AF XY: 0.220 AC XY: 16326 AN XY: 74348

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.226

Alfa AF: 0.235 Hom.: 7186

Bravo AF: 0.223

Asia WGS AF: 0.187 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
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: rs665579; hg19: chr5-62811418;