rs6504909

Variant names:

• chr17-54470764-A-G
• rs6504909

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 0.331 in 152,004 control chromosomes in the GnomAD database, including 11,410 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 0.33 (11410 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50204 AN: 151886 Hom.: 11383 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.331 AC: 50277 AN: 152004 Hom.: 11410 Cov.: 32 AF XY: 0.325 AC XY: 24107 AN XY: 74284

African (AFR) AF: 0.645 AC: 26718 AN: 41428

American (AMR) AF: 0.218 AC: 3332 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3472

East Asian (EAS) AF: 0.0515 AC: 266 AN: 5162

South Asian (SAS) AF: 0.153 AC: 737 AN: 4822

European-Finnish (FIN) AF: 0.237 AC: 2505 AN: 10566

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15213 AN: 67962

Other (OTH) AF: 0.264 AC: 558 AN: 2112

Alfa AF: 0.251 Hom.: 26075

Bravo AF: 0.342

Asia WGS AF: 0.140 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.45
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs6504909; hg19: chr17-52548125;