chr17-63889105-C-G

Variant names:

• chr17-63889105-C-G
• rs2665838

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 0.236 in 151,960 control chromosomes in the GnomAD database, including 4,627 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 0.24 (4627 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 51 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35890 AN: 151842 Hom.: 4620 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.236 AC: 35896 AN: 151960 Hom.: 4627 Cov.: 32 AF XY: 0.231 AC XY: 17179 AN XY: 74290

African (AFR) AF: 0.229 AC: 9504 AN: 41452

American (AMR) AF: 0.196 AC: 2995 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 907 AN: 3470

East Asian (EAS) AF: 0.0604 AC: 313 AN: 5184

South Asian (SAS) AF: 0.168 AC: 810 AN: 4820

European-Finnish (FIN) AF: 0.202 AC: 2135 AN: 10590

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18371 AN: 67892

Other (OTH) AF: 0.245 AC: 515 AN: 2102

Alfa AF: 0.131 Hom.: 245

Bravo AF: 0.236

Asia WGS AF: 0.127 AC: 445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.62
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2665838; hg19: chr17-61966465;