rs6450583

Positions:

• chr5-17680610-A-G
• chr5-17680610-A-T

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 0.223 in 152,130 control chromosomes in the GnomAD database, including 4,576 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 (4576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 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: 0.223 AC: 33933 AN: 152012 Hom.: 4572 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.223 AC: 33957 AN: 152130 Hom.: 4576 Cov.: 32 AF XY: 0.230 AC XY: 17114 AN XY: 74346

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.229

Alfa AF: 0.236 Hom.: 2266

Bravo AF: 0.228

Asia WGS AF: 0.377 AC: 1306 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6450583; hg19: chr5-17680719;