17-12665159-C-G

Variant names:

• chr17-12665159-C-G
• rs1233851

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 0.0242 in 152,282 control chromosomes in the GnomAD database, including 53 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 0.024 (53 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0744 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: 0.0242 AC: 3680 AN: 152164 Hom.: 53 Cov.: 32

Gnomad AFR AF: 0.00632

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0218

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0805

Gnomad FIN AF: 0.0324

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0308

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0242 AC: 3684 AN: 152282 Hom.: 53 Cov.: 32 AF XY: 0.0249 AC XY: 1854 AN XY: 74450

African (AFR) AF: 0.00635 AC: 264 AN: 41568

American (AMR) AF: 0.0218 AC: 333 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3472

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5166

South Asian (SAS) AF: 0.0810 AC: 390 AN: 4816

European-Finnish (FIN) AF: 0.0324 AC: 344 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0308 AC: 2095 AN: 68024

Other (OTH) AF: 0.0393 AC: 83 AN: 2114

Alfa AF: 0.0133 Hom.: 4

Bravo AF: 0.0216

Asia WGS AF: 0.0680 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.9
DANN	Benign	0.46
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1233851; hg19: chr17-12568476; COSMIC: COSV58510949;