rs6450583

Variant names:

• chr5-17680610-A-G
• rs6450583

Your query was ambiguous. Multiple possible variants found:

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

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 0.223 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.119 AC: 4921 AN: 41512

American (AMR) AF: 0.368 AC: 5618 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3472

East Asian (EAS) AF: 0.525 AC: 2710 AN: 5158

South Asian (SAS) AF: 0.300 AC: 1449 AN: 4822

European-Finnish (FIN) AF: 0.257 AC: 2726 AN: 10596

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15225 AN: 67982

Other (OTH) AF: 0.229 AC: 483 AN: 2112

Alfa AF: 0.234 Hom.: 2492

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
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs6450583; hg19: chr5-17680719;